Gauge coupling unification in realistic free-fermionic string models

International Nuclear Information System (INIS)

Dienes, K.R.; Faraggi, A.E.

1995-01-01

We discuss the unification of gauge couplings within the framework of a wide class of realistic free-fermionic string models which have appeared in the literature, including the flipped SU(5), SO(6)xSO(4), and various SU(3)xSU(2)xU(1) models. If the matter spectrum below the string scale is that of the Minimal Supersymmetric Standard Model (MSSM), then string unification is in disagreement with experiment. We therefore examine several effects that may modify the minimal string predictions. First, we develop a systematic procedure for evaluating the one-loop heavy string threshold corrections in free-fermionic string models, and we explicitly evaluate these corrections for each of the realistic models. We find that these string threshold corrections are small, and we provide general arguments explaining why such threshold corrections are suppressed in string theory. Thus heavy thresholds cannot resolve the disagreement with experiment. We also study the effect of non-standard hypercharge normalizations, light SUSY thresholds, and intermediate-scale gauge structure, and similarly conclude that these effects cannot resolve the disagreement with low-energy data. Finally, we examine the effects of additional color triplets and electroweak doublets beyond the MSSM. Although not required in ordinary grand unification scenarios, such states generically appear within the context of certain realistic free-fermionic string models. We show that if these states exist at the appropriate thresholds, then the gauge couplings will indeed unify at the string scale. Thus, within these string models, string unification can be in agreement with low-energy data. (orig.)

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

DEFF Research Database (Denmark)

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

2016-01-01

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

Realistic Gamow shell model for resonance and continuum in atomic nuclei

Science.gov (United States)

Xu, F. R.; Sun, Z. H.; Wu, Q.; Hu, B. S.; Dai, S. J.

2018-02-01

The Gamow shell model can describe resonance and continuum for atomic nuclei. The model is established in the complex-moment (complex-k) plane of the Berggren coordinates in which bound, resonant and continuum states are treated on equal footing self-consistently. In the present work, the realistic nuclear force, CD Bonn, has been used. We have developed the full \\hat{Q}-box folded-diagram method to derive the realistic effective interaction in the model space which is nondegenerate and contains resonance and continuum channels. The CD-Bonn potential is renormalized using the V low-k method. With choosing 16O as the inert core, we have applied the Gamow shell model to oxygen isotopes.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

Science.gov (United States)

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Modeling of ultrasonic wave propagation in composite laminates with realistic discontinuity representation.

Science.gov (United States)

Zelenyak, Andreea-Manuela; Schorer, Nora; Sause, Markus G R

2018-02-01

This paper presents a method for embedding realistic defect geometries of a fiber reinforced material in a finite element modeling environment in order to simulate active ultrasonic inspection. When ultrasonic inspection is used experimentally to investigate the presence of defects in composite materials, the microscopic defect geometry may cause signal characteristics that are difficult to interpret. Hence, modeling of this interaction is key to improve our understanding and way of interpreting the acquired ultrasonic signals. To model the true interaction of the ultrasonic wave field with such defect structures as pores, cracks or delamination, a realistic three dimensional geometry reconstruction is required. We present a 3D-image based reconstruction process which converts computed tomography data in adequate surface representations ready to be embedded for processing with finite element methods. Subsequent modeling using these geometries uses a multi-scale and multi-physics simulation approach which results in quantitative A-Scan ultrasonic signals which can be directly compared with experimental signals. Therefore, besides the properties of the composite material, a full transducer implementation, piezoelectric conversion and simultaneous modeling of the attached circuit is applied. Comparison between simulated and experimental signals provides very good agreement in electrical voltage amplitude and the signal arrival time and thus validates the proposed modeling approach. Simulating ultrasound wave propagation in a medium with a realistic shape of the geometry clearly shows a difference in how the disturbance of the waves takes place and finally allows more realistic modeling of A-scans. Copyright © 2017 Elsevier B.V. All rights reserved.

An Overview of Westinghouse Realistic Large Break LOCA Evaluation Model

Directory of Open Access Journals (Sweden)

Cesare Frepoli

2008-01-01

Full Text Available Since the 1988 amendment of the 10 CFR 50.46 rule in 1988, Westinghouse has been developing and applying realistic or best-estimate methods to perform LOCA safety analyses. A realistic analysis requires the execution of various realistic LOCA transient simulations where the effect of both model and input uncertainties are ranged and propagated throughout the transients. The outcome is typically a range of results with associated probabilities. The thermal/hydraulic code is the engine of the methodology but a procedure is developed to assess the code and determine its biases and uncertainties. In addition, inputs to the simulation are also affected by uncertainty and these uncertainties are incorporated into the process. Several approaches have been proposed and applied in the industry in the framework of best-estimate methods. Most of the implementations, including Westinghouse, follow the Code Scaling, Applicability and Uncertainty (CSAU methodology. Westinghouse methodology is based on the use of the WCOBRA/TRAC thermal-hydraulic code. The paper starts with an overview of the regulations and its interpretation in the context of realistic analysis. The CSAU roadmap is reviewed in the context of its implementation in the Westinghouse evaluation model. An overview of the code (WCOBRA/TRAC and methodology is provided. Finally, the recent evolution to nonparametric statistics in the current edition of the W methodology is discussed. Sample results of a typical large break LOCA analysis for a PWR are provided.

Plasticity-modulated seizure dynamics for seizure termination in realistic neuronal models

NARCIS (Netherlands)

Koppert, M.M.J.; Kalitzin, S.; Lopes da Silva, F.H.; Viergever, M.A.

2011-01-01

In previous studies we showed that autonomous absence seizure generation and termination can be explained by realistic neuronal models eliciting bi-stable dynamics. In these models epileptic seizures are triggered either by external stimuli (reflex epilepsies) or by internal fluctuations. This

Automatic procedure for realistic 3D finite element modelling of human brain for bioelectromagnetic computations

International Nuclear Information System (INIS)

Aristovich, K Y; Khan, S H

2010-01-01

Realistic computer modelling of biological objects requires building of very accurate and realistic computer models based on geometric and material data, type, and accuracy of numerical analyses. This paper presents some of the automatic tools and algorithms that were used to build accurate and realistic 3D finite element (FE) model of whole-brain. These models were used to solve the forward problem in magnetic field tomography (MFT) based on Magnetoencephalography (MEG). The forward problem involves modelling and computation of magnetic fields produced by human brain during cognitive processing. The geometric parameters of the model were obtained from accurate Magnetic Resonance Imaging (MRI) data and the material properties - from those obtained from Diffusion Tensor MRI (DTMRI). The 3D FE models of the brain built using this approach has been shown to be very accurate in terms of both geometric and material properties. The model is stored on the computer in Computer-Aided Parametrical Design (CAD) format. This allows the model to be used in a wide a range of methods of analysis, such as finite element method (FEM), Boundary Element Method (BEM), Monte-Carlo Simulations, etc. The generic model building approach presented here could be used for accurate and realistic modelling of human brain and many other biological objects.

Development of vortex model with realistic axial velocity distribution

International Nuclear Information System (INIS)

Ito, Kei; Ezure, Toshiki; Ohshima, Hiroyuki

2014-01-01

A vortex is considered as one of significant phenomena which may cause gas entrainment (GE) and/or vortex cavitation in sodium-cooled fast reactors. In our past studies, the vortex is assumed to be approximated by the well-known Burgers vortex model. However, the Burgers vortex model has a simple but unreal assumption that the axial velocity component is horizontally constant, while in real the free surface vortex has the axial velocity distribution which shows large gradient in radial direction near the vortex center. In this study, a new vortex model with realistic axial velocity distribution is proposed. This model is derived from the steady axisymmetric Navier-Stokes equation as well as the Burgers vortex model, but the realistic axial velocity distribution in radial direction is considered, which is defined to be zero at the vortex center and to approach asymptotically to zero at infinity. As the verification, the new vortex model is applied to the evaluation of a simple vortex experiment, and shows good agreements with the experimental data in terms of the circumferential velocity distribution and the free surface shape. In addition, it is confirmed that the Burgers vortex model fails to calculate accurate velocity distribution with the assumption of uniform axial velocity. However, the calculation accuracy of the Burgers vortex model can be enhanced close to that of the new vortex model in consideration of the effective axial velocity which is calculated as the average value only in the vicinity of the vortex center. (author)

Realistic shell-model calculations for Sn isotopes

International Nuclear Information System (INIS)

Covello, A.; Andreozzi, F.; Coraggio, L.; Gargano, A.; Porrino, A.

1997-01-01

We report on a shell-model study of the Sn isotopes in which a realistic effective interaction derived from the Paris free nucleon-nucleon potential is employed. The calculations are performed within the framework of the seniority scheme by making use of the chain-calculation method. This provides practically exact solutions while cutting down the amount of computational work required by a standard seniority-truncated calculation. The behavior of the energy of several low-lying states in the isotopes with A ranging from 122 to 130 is presented and compared with the experimental one. (orig.)

Simplified realistic human head model for simulating Tumor Treating Fields (TTFields).

Science.gov (United States)

Wenger, Cornelia; Bomzon, Ze'ev; Salvador, Ricardo; Basser, Peter J; Miranda, Pedro C

2016-08-01

Tumor Treating Fields (TTFields) are alternating electric fields in the intermediate frequency range (100-300 kHz) of low-intensity (1-3 V/cm). TTFields are an anti-mitotic treatment against solid tumors, which are approved for Glioblastoma Multiforme (GBM) patients. These electric fields are induced non-invasively by transducer arrays placed directly on the patient's scalp. Cell culture experiments showed that treatment efficacy is dependent on the induced field intensity. In clinical practice, a software called NovoTalTM uses head measurements to estimate the optimal array placement to maximize the electric field delivery to the tumor. Computational studies predict an increase in the tumor's electric field strength when adapting transducer arrays to its location. Ideally, a personalized head model could be created for each patient, to calculate the electric field distribution for the specific situation. Thus, the optimal transducer layout could be inferred from field calculation rather than distance measurements. Nonetheless, creating realistic head models of patients is time-consuming and often needs user interaction, because automated image segmentation is prone to failure. This study presents a first approach to creating simplified head models consisting of convex hulls of the tissue layers. The model is able to account for anisotropic conductivity in the cortical tissues by using a tensor representation estimated from Diffusion Tensor Imaging. The induced electric field distribution is compared in the simplified and realistic head models. The average field intensities in the brain and tumor are generally slightly higher in the realistic head model, with a maximal ratio of 114% for a simplified model with reasonable layer thicknesses. Thus, the present pipeline is a fast and efficient means towards personalized head models with less complexity involved in characterizing tissue interfaces, while enabling accurate predictions of electric field distribution.

Realistic modeling of chamber transport for heavy-ion fusion

International Nuclear Information System (INIS)

Sharp, W.M.; Grote, D.P.; Callahan, D.A.; Tabak, M.; Henestroza, E.; Yu, S.S.; Peterson, P.F.; Welch, D.R.; Rose, D.V.

2003-01-01

Transport of intense heavy-ion beams to an inertial-fusion target after final focus is simulated here using a realistic computer model. It is found that passing the beam through a rarefied plasma layer before it enters the fusion chamber can largely neutralize the beam space charge and lead to a usable focal spot for a range of ion species and input conditions

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

Science.gov (United States)

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

2014-12-19

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

Electron percolation in realistic models of carbon nanotube networks

International Nuclear Information System (INIS)

Simoneau, Louis-Philippe; Villeneuve, Jérémie; Rochefort, Alain

2015-01-01

The influence of penetrable and curved carbon nanotubes (CNT) on the charge percolation in three-dimensional disordered CNT networks have been studied with Monte-Carlo simulations. By considering carbon nanotubes as solid objects but where the overlap between their electron cloud can be controlled, we observed that the structural characteristics of networks containing lower aspect ratio CNT are highly sensitive to the degree of penetration between crossed nanotubes. Following our efficient strategy to displace CNT to different positions to create more realistic statistical models, we conclude that the connectivity between objects increases with the hard-core/soft-shell radii ratio. In contrast, the presence of curved CNT in the random networks leads to an increasing percolation threshold and to a decreasing electrical conductivity at saturation. The waviness of CNT decreases the effective distance between the nanotube extremities, hence reducing their connectivity and degrading their electrical properties. We present the results of our simulation in terms of thickness of the CNT network from which simple structural parameters such as the volume fraction or the carbon nanotube density can be accurately evaluated with our more realistic models

Electron percolation in realistic models of carbon nanotube networks

Science.gov (United States)

Simoneau, Louis-Philippe; Villeneuve, Jérémie; Rochefort, Alain

2015-09-01

The influence of penetrable and curved carbon nanotubes (CNT) on the charge percolation in three-dimensional disordered CNT networks have been studied with Monte-Carlo simulations. By considering carbon nanotubes as solid objects but where the overlap between their electron cloud can be controlled, we observed that the structural characteristics of networks containing lower aspect ratio CNT are highly sensitive to the degree of penetration between crossed nanotubes. Following our efficient strategy to displace CNT to different positions to create more realistic statistical models, we conclude that the connectivity between objects increases with the hard-core/soft-shell radii ratio. In contrast, the presence of curved CNT in the random networks leads to an increasing percolation threshold and to a decreasing electrical conductivity at saturation. The waviness of CNT decreases the effective distance between the nanotube extremities, hence reducing their connectivity and degrading their electrical properties. We present the results of our simulation in terms of thickness of the CNT network from which simple structural parameters such as the volume fraction or the carbon nanotube density can be accurately evaluated with our more realistic models.

A scan for models with realistic fermion mass patterns

International Nuclear Information System (INIS)

Bijnens, J.; Wetterich, C.

1986-03-01

We consider models which have no small Yukawa couplings unrelated to symmetry. This situation is generic in higher dimensional unification where Yukawa couplings are predicted to have strength similar to the gauge couplings. Generations have then to be differentiated by symmetry properties and the structure of fermion mass matrices is given in terms of quantum numbers alone. We scan possible symmetries leading to realistic mass matrices. (orig.)

Comparing Realistic Subthalamic Nucleus Neuron Models

Science.gov (United States)

Njap, Felix; Claussen, Jens C.; Moser, Andreas; Hofmann, Ulrich G.

2011-06-01

The mechanism of action of clinically effective electrical high frequency stimulation is still under debate. However, recent evidence points at the specific activation of GABA-ergic ion channels. Using a computational approach, we analyze temporal properties of the spike trains emitted by biologically realistic neurons of the subthalamic nucleus (STN) as a function of GABA-ergic synaptic input conductances. Our contribution is based on a model proposed by Rubin and Terman and exhibits a wide variety of different firing patterns, silent, low spiking, moderate spiking and intense spiking activity. We observed that most of the cells in our network turn to silent mode when we increase the GABAA input conductance above the threshold of 3.75 mS/cm2. On the other hand, insignificant changes in firing activity are observed when the input conductance is low or close to zero. We thus reproduce Rubin's model with vanishing synaptic conductances. To quantitatively compare spike trains from the original model with the modified model at different conductance levels, we apply four different (dis)similarity measures between them. We observe that Mahalanobis distance, Victor-Purpura metric, and Interspike Interval distribution are sensitive to different firing regimes, whereas Mutual Information seems undiscriminative for these functional changes.

Toward developing more realistic groundwater models using big data

Science.gov (United States)

Vahdat Aboueshagh, H.; Tsai, F. T. C.; Bhatta, D.; Paudel, K.

2017-12-01

Rich geological data is the backbone of developing realistic groundwater models for groundwater resources management. However, constructing realistic groundwater models can be challenging due to inconsistency between different sources of geological, hydrogeological and geophysical data and difficulty in processing big data to characterize the subsurface environment. This study develops a framework to utilize a big geological dataset to create a groundwater model for the Chicot Aquifer in the southwestern Louisiana, which borders on the Gulf of Mexico at south. The Chicot Aquifer is the principal source of fresh water in southwest Louisiana, underlying an area of about 9,000 square miles. Agriculture is the largest groundwater consumer in this region and overpumping has caused significant groundwater head decline and saltwater intrusion from the Gulf and deep formations. A hydrostratigraphy model was constructed using around 29,000 electrical logs and drillers' logs as well as screen lengths of pumping wells through a natural neighbor interpolation method. These sources of information have different weights in terms of accuracy and trustworthy. A data prioritization procedure was developed to filter untrustworthy log information, eliminate redundant data, and establish consensus of various lithological information. The constructed hydrostratigraphy model shows 40% sand facies, which is consistent with the well log data. The hydrostratigraphy model confirms outcrop areas of the Chicot Aquifer in the north of the study region. The aquifer sand formation is thinning eastward to merge into Atchafalaya River alluvial aquifer and coalesces to the underlying Evangeline aquifer. A grid generator was used to convert the hydrostratigraphy model into a MODFLOW grid with 57 layers. A Chicot groundwater model was constructed using the available hydrologic and hydrogeological data for 2004-2015. Pumping rates for irrigation wells were estimated using the crop type and acreage

Modeling and Analysis of Realistic Fire Scenarios in Spacecraft

Science.gov (United States)

Brooker, J. E.; Dietrich, D. L.; Gokoglu, S. A.; Urban, D. L.; Ruff, G. A.

2015-01-01

An accidental fire inside a spacecraft is an unlikely, but very real emergency situation that can easily have dire consequences. While much has been learned over the past 25+ years of dedicated research on flame behavior in microgravity, a quantitative understanding of the initiation, spread, detection and extinguishment of a realistic fire aboard a spacecraft is lacking. Virtually all combustion experiments in microgravity have been small-scale, by necessity (hardware limitations in ground-based facilities and safety concerns in space-based facilities). Large-scale, realistic fire experiments are unlikely for the foreseeable future (unlike in terrestrial situations). Therefore, NASA will have to rely on scale modeling, extrapolation of small-scale experiments and detailed numerical modeling to provide the data necessary for vehicle and safety system design. This paper presents the results of parallel efforts to better model the initiation, spread, detection and extinguishment of fires aboard spacecraft. The first is a detailed numerical model using the freely available Fire Dynamics Simulator (FDS). FDS is a CFD code that numerically solves a large eddy simulation form of the Navier-Stokes equations. FDS provides a detailed treatment of the smoke and energy transport from a fire. The simulations provide a wealth of information, but are computationally intensive and not suitable for parametric studies where the detailed treatment of the mass and energy transport are unnecessary. The second path extends a model previously documented at ICES meetings that attempted to predict maximum survivable fires aboard space-craft. This one-dimensional model implies the heat and mass transfer as well as toxic species production from a fire. These simplifications result in a code that is faster and more suitable for parametric studies (having already been used to help in the hatch design of the Multi-Purpose Crew Vehicle, MPCV).

Solubility of gases and solvents in silicon polymers: molecular simulation and equation of state modeling

DEFF Research Database (Denmark)

Economou, Ioannis; Makrodimitri, Zoi A.; Kontogeorgis, Georgios

2007-01-01

of gas and solvent solubilities using the test particle insertion method of Widom. Polymer chains are modelled using recently developed realistic atomistic force fields. Calculations are performed at various temperatures and ambient pressure. A crossover in the temperature dependence of solubility......) and also the phase equilibria of these mixtures over a wide composition range. In all cases, the agreement between model predictions/correlations and literature experimental data, when available, is excellent.......The solubility of n-alkanes, perfluoroalkanes, noble gases and light gases in four elastomer polymers containing silicon is examined based on molecular simulation and macroscopic equation of state modelling. Polymer melt samples generated from molecular dynamics ( MD) are used for the calculation...

Triangulating and guarding realistic polygons

NARCIS (Netherlands)

Aloupis, G.; Bose, P.; Dujmovic, V.; Gray, C.M.; Langerman, S.; Speckmann, B.

2014-01-01

We propose a new model of realistic input: k-guardable objects. An object is k-guardable if its boundary can be seen by k guards. We show that k-guardable polygons generalize two previously identified classes of realistic input. Following this, we give two simple algorithms for triangulating

Realistic modeling of seismic input for megacities and large urban areas

International Nuclear Information System (INIS)

Panza, Giuliano F.; Alvarez, Leonardo; Aoudia, Abdelkrim

2002-06-01

The project addressed the problem of pre-disaster orientation: hazard prediction, risk assessment, and hazard mapping, in connection with seismic activity and man-induced vibrations. The definition of realistic seismic input has been obtained from the computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different source and structural models. The innovative modeling technique, that constitutes the common tool to the entire project, takes into account source, propagation and local site effects. This is done using first principles of physics about wave generation and propagation in complex media, and does not require to resort to convolutive approaches, that have been proven to be quite unreliable, mainly when dealing with complex geological structures, the most interesting from the practical point of view. In fact, several techniques that have been proposed to empirically estimate the site effects using observations convolved with theoretically computed signals corresponding to simplified models, supply reliable information about the site response to non-interfering seismic phases. They are not adequate in most of the real cases, when the seismic sequel is formed by several interfering waves. The availability of realistic numerical simulations enables us to reliably estimate the amplification effects even in complex geological structures, exploiting the available geotechnical, lithological, geophysical parameters, topography of the medium, tectonic, historical, palaeoseismological data, and seismotectonic models. The realistic modeling of the ground motion is a very important base of knowledge for the preparation of groundshaking scenarios that represent a valid and economic tool for the seismic microzonation. This knowledge can be very fruitfully used by civil engineers in the design of new seismo-resistant constructions and in the reinforcement of the existing built environment, and, therefore

Realistic Avatar Eye and Head Animation Using a Neurobiological Model of Visual Attention

National Research Council Canada - National Science Library

Itti, L; Dhavale, N; Pighin, F

2003-01-01

We describe a neurobiological model of visual attention and eye/head movements in primates, and its application to the automatic animation of a realistic virtual human head watching an unconstrained...

Finite Time Blowup in a Realistic Food-Chain Model

KAUST Repository

Parshad, Rana; Ait Abderrahmane, Hamid; Upadhyay, Ranjit Kumar; Kumari, Nitu

2013-01-01

We investigate a realistic three-species food-chain model, with generalist top predator. The model based on a modified version of the Leslie-Gower scheme incorporates mutual interference in all the three populations and generalizes several other known models in the ecological literature. We show that the model exhibits finite time blowup in certain parameter range and for large enough initial data. This result implies that finite time blowup is possible in a large class of such three-species food-chain models. We propose a modification to the model and prove that the modified model has globally existing classical solutions, as well as a global attractor. We reconstruct the attractor using nonlinear time series analysis and show that it pssesses rich dynamics, including chaos in certain parameter regime, whilst avoiding blowup in any parameter regime. We also provide estimates on its fractal dimension as well as provide numerical simulations to visualise the spatiotemporal chaos.

Finite Time Blowup in a Realistic Food-Chain Model

KAUST Repository

Parshad, Rana

2013-05-19

We investigate a realistic three-species food-chain model, with generalist top predator. The model based on a modified version of the Leslie-Gower scheme incorporates mutual interference in all the three populations and generalizes several other known models in the ecological literature. We show that the model exhibits finite time blowup in certain parameter range and for large enough initial data. This result implies that finite time blowup is possible in a large class of such three-species food-chain models. We propose a modification to the model and prove that the modified model has globally existing classical solutions, as well as a global attractor. We reconstruct the attractor using nonlinear time series analysis and show that it pssesses rich dynamics, including chaos in certain parameter regime, whilst avoiding blowup in any parameter regime. We also provide estimates on its fractal dimension as well as provide numerical simulations to visualise the spatiotemporal chaos.

Development of Realistic Head Models for Electromagnetic Source Imaging of the Human Brain

National Research Council Canada - National Science Library

Akalin, Z

2001-01-01

In this work, a methodology is developed to solve the forward problem of electromagnetic source imaging using realistic head models, For this purpose, first segmentation of the 3 dimensional MR head...

Realistic modelling of the seismic input: Site effects and parametric studies

International Nuclear Information System (INIS)

Romanelli, F.; Vaccari, F.; Panza, G.F.

2002-11-01

We illustrate the work done in the framework of a large international cooperation, showing the very recent numerical experiments carried out within the framework of the EC project 'Advanced methods for assessing the seismic vulnerability of existing motorway bridges' (VAB) to assess the importance of non-synchronous seismic excitation of long structures. The definition of the seismic input at the Warth bridge site, i.e. the determination of the seismic ground motion due to an earthquake with a given magnitude and epicentral distance from the site, has been done following a theoretical approach. In order to perform an accurate and realistic estimate of site effects and of differential motion it is necessary to make a parametric study that takes into account the complex combination of the source and propagation parameters, in realistic geological structures. The computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different sources and structural models, allows us the construction of damage scenarios that are out of the reach of stochastic models, at a very low cost/benefit ratio. (author)

Bringing molecules back into molecular evolution.

Directory of Open Access Journals (Sweden)

Claus O Wilke

Full Text Available Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

Integrative computational models of cardiac arrhythmias -- simulating the structurally realistic heart

Science.gov (United States)

Trayanova, Natalia A; Tice, Brock M

2009-01-01

Simulation of cardiac electrical function, and specifically, simulation aimed at understanding the mechanisms of cardiac rhythm disorders, represents an example of a successful integrative multiscale modeling approach, uncovering emergent behavior at the successive scales in the hierarchy of structural complexity. The goal of this article is to present a review of the integrative multiscale models of realistic ventricular structure used in the quest to understand and treat ventricular arrhythmias. It concludes with the new advances in image-based modeling of the heart and the promise it holds for the development of individualized models of ventricular function in health and disease. PMID:20628585

IBM parameters derived from realistic shell-model Hamiltonian via Hn-cooling method

International Nuclear Information System (INIS)

Nakada, Hitoshi

1997-01-01

There is a certain influence of non-collective degrees-of-freedom even in lowest-lying states of medium-heavy nuclei. This influence seems to be significant for some of the IBM parameters. In order to take it into account, several renormalization approaches have been applied. It has been shown in the previous studies that the influence of the G-pairs is important, but does not fully account for the fitted values. The influence of the non-collective components may be more serious when we take a realistic effective nucleonic interaction. To incorporate this influence into the IBM parameters, we employ the recently developed H n -cooling method. This method is applied to renormalize the wave functions of the states consisting of the SD-pairs, for the Cr-Fe nuclei. On this ground, the IBM Hamiltonian and transition operators are derived from corresponding realistic shell-model operators, for the Cr-Fe nuclei. Together with some features of the realistic interaction, the effects of the non-SD degrees-of-freedom are presented. (author)

Realistic Visualization of Virtual Views

DEFF Research Database (Denmark)

Livatino, Salvatore

2005-01-01

that can be impractical and sometime impossible. In addition, the artificial nature of data often makes visualized virtual scenarios not realistic enough. Not realistic in the sense that a synthetic scene is easy to discriminate visually from a natural scene. A new field of research has consequently...... developed and received much attention in recent years: Realistic Virtual View Synthesis. The main goal is a high fidelity representation of virtual scenarios while easing modeling and physical phenomena simulation. In particular, realism is achieved by the transfer to the novel view of all the physical...... phenomena captured in the reference photographs, (i.e. the transfer of photographic-realism). An overview of most prominent approaches in realistic virtual view synthesis will be presented and briefly discussed. Applications of proposed methods to visual survey, virtual cinematography, as well as mobile...

Correcting electrode modelling errors in EIT on realistic 3D head models.

Science.gov (United States)

Jehl, Markus; Avery, James; Malone, Emma; Holder, David; Betcke, Timo

2015-12-01

Electrical impedance tomography (EIT) is a promising medical imaging technique which could aid differentiation of haemorrhagic from ischaemic stroke in an ambulance. One challenge in EIT is the ill-posed nature of the image reconstruction, i.e., that small measurement or modelling errors can result in large image artefacts. It is therefore important that reconstruction algorithms are improved with regard to stability to modelling errors. We identify that wrongly modelled electrode positions constitute one of the biggest sources of image artefacts in head EIT. Therefore, the use of the Fréchet derivative on the electrode boundaries in a realistic three-dimensional head model is investigated, in order to reconstruct electrode movements simultaneously to conductivity changes. We show a fast implementation and analyse the performance of electrode position reconstructions in time-difference and absolute imaging for simulated and experimental voltages. Reconstructing the electrode positions and conductivities simultaneously increased the image quality significantly in the presence of electrode movement.

Processing of the GALILEO fuel rod code model uncertainties within the AREVA LWR realistic thermal-mechanical analysis methodology

International Nuclear Information System (INIS)

Mailhe, P.; Barbier, B.; Garnier, C.; Landskron, H.; Sedlacek, R.; Arimescu, I.; Smith, M.; Bellanger, P.

2013-01-01

The availability of reliable tools and associated methodology able to accurately predict the LWR fuel behavior in all conditions is of great importance for safe and economic fuel usage. For that purpose, AREVA has developed its new global fuel rod performance code GALILEO along with its associated realistic thermal-mechanical analysis methodology. This realistic methodology is based on a Monte Carlo type random sampling of all relevant input variables. After having outlined the AREVA realistic methodology, this paper will be focused on the GALILEO code benchmarking process, on its extended experimental database and on the GALILEO model uncertainties assessment. The propagation of these model uncertainties through the AREVA realistic methodology is also presented. This GALILEO model uncertainties processing is of the utmost importance for accurate fuel design margin evaluation as illustrated on some application examples. With the submittal of Topical Report GALILEO to the U.S. NRC in 2013, GALILEO and its methodology are on the way to be industrially used in a wide range of irradiation conditions. (authors)

Radiation Damage to Nervous System: Designing Optimal Models for Realistic Neuron Morphology in Hippocampus

Science.gov (United States)

Batmunkh, Munkhbaatar; Bugay, Alexander; Bayarchimeg, Lkhagvaa; Lkhagva, Oidov

2018-02-01

The present study is focused on the development of optimal models of neuron morphology for Monte Carlo microdosimetry simulations of initial radiation-induced events of heavy charged particles in the specific types of cells of the hippocampus, which is the most radiation-sensitive structure of the central nervous system. The neuron geometry and particles track structures were simulated by the Geant4/Geant4-DNA Monte Carlo toolkits. The calculations were made for beams of protons and heavy ions with different energies and doses corresponding to real fluxes of galactic cosmic rays. A simple compartmental model and a complex model with realistic morphology extracted from experimental data were constructed and compared. We estimated the distribution of the energy deposition events and the production of reactive chemical species within the developed models of CA3/CA1 pyramidal neurons and DG granule cells of the rat hippocampus under exposure to different particles with the same dose. Similar distributions of the energy deposition events and concentration of some oxidative radical species were obtained in both the simplified and realistic neuron models.

Any realistic theory must be computationally realistic: a response to N. Gisin's definition of a Realistic Physics Theory

OpenAIRE

Bolotin, Arkady

2014-01-01

It is argued that the recent definition of a realistic physics theory by N. Gisin cannot be considered comprehensive unless it is supplemented with requirement that any realistic theory must be computationally realistic as well.

Simulation of size-dependent aerosol deposition in a realistic model of the upper human airways

NARCIS (Netherlands)

Frederix, E.M.A.; Kuczaj, Arkadiusz K.; Nordlund, Markus; Belka, M.; Lizal, F.; Elcner, J.; Jicha, M.; Geurts, Bernardus J.

An Eulerian internally mixed aerosol model is used for predictions of deposition inside a realistic cast of the human upper airways. The model, formulated in the multi-species and compressible framework, is solved using the sectional discretization of the droplet size distribution function to

Bell Operator Method to Classify Local Realistic Theories

International Nuclear Information System (INIS)

Nagata, Koji

2010-01-01

We review the historical fact of multipartite Bell inequalities with an arbitrary number of settings. An explicit local realistic model for the values of a correlation function, given in a two-setting Bell experiment (two-setting model), works only for the specific set of settings in the given experiment, but cannot construct a local realistic model for the values of a correlation function, given in a continuous-infinite settings Bell experiment (infinite-setting model), even though there exist two-setting models for all directions in space. Hence, the two-setting model does not have the property that the infinite-setting model has. Here, we show that an explicit two-setting model cannot construct a local realistic model for the values of a correlation function, given in an M-setting Bell experiment (M-setting model), even though there exist two-setting models for the M measurement directions chosen in the given M-setting experiment. Hence, the two-setting model does not have the property that the M-setting model has. (general)

Modelling Analysis of Echo Signature and Target Strength of a Realistically Modelled Ship Wake for a Generic Forward Looking Active Sonar

NARCIS (Netherlands)

Schippers, P.

2009-01-01

The acoustic modelling in TNO’s ALMOST (=Acoustic Loss Model for Operational Studies and Tasks) uses a bubble migration model as realistic input for wake modelling. The modelled bubble cloud represents the actual ship wake. Ship hull, propeller and bow wave are the main generators of bubbles in the

Statistical multi-path exposure method for assessing the whole-body SAR in a heterogeneous human body model in a realistic environment.

Science.gov (United States)

Vermeeren, Günter; Joseph, Wout; Martens, Luc

2013-04-01

Assessing the whole-body absorption in a human in a realistic environment requires a statistical approach covering all possible exposure situations. This article describes the development of a statistical multi-path exposure method for heterogeneous realistic human body models. The method is applied for the 6-year-old Virtual Family boy (VFB) exposed to the GSM downlink at 950 MHz. It is shown that the whole-body SAR does not differ significantly over the different environments at an operating frequency of 950 MHz. Furthermore, the whole-body SAR in the VFB for multi-path exposure exceeds the whole-body SAR for worst-case single-incident plane wave exposure by 3.6%. Moreover, the ICNIRP reference levels are not conservative with the basic restrictions in 0.3% of the exposure samples for the VFB at the GSM downlink of 950 MHz. The homogeneous spheroid with the dielectric properties of the head suggested by the IEC underestimates the absorption compared to realistic human body models. Moreover, the variation in the whole-body SAR for realistic human body models is larger than for homogeneous spheroid models. This is mainly due to the heterogeneity of the tissues and the irregular shape of the realistic human body model compared to homogeneous spheroid human body models. Copyright © 2012 Wiley Periodicals, Inc.

Fault-Tolerant Robot Programming through Simulation with Realistic Sensor Models

Directory of Open Access Journals (Sweden)

Axel Waggershauser

2008-11-01

Full Text Available We introduce a simulation system for mobile robots that allows a realistic interaction of multiple robots in a common environment. The simulated robots are closely modeled after robots from the EyeBot family and have an identical application programmer interface. The simulation supports driving commands at two levels of abstraction as well as numerous sensors such as shaft encoders, infrared distance sensors, and compass. Simulation of on-board digital cameras via synthetic images allows the use of image processing routines for robot control within the simulation. Specific error models for actuators, distance sensors, camera sensor, and wireless communication have been implemented. Progressively increasing error levels for an application program allows for testing and improving its robustness and fault-tolerance.

High resolution color raster computer animation of space filling molecular models

Energy Technology Data Exchange (ETDEWEB)

Max, N.L.

1981-01-01

The ATOMLLL system efficiently produces realistic photographs of ball-and-stick or space-filling molecular models, with color shading, highlights, shadows, and transparency. The hidden surface problem for a scene composed of intersecting spheres and cylinders is solved on a CDC-7600, which outputs onto magnetic tape the outlines of the visible parts of each object. The outlines are then rendered, at up to 4096 x 4096 resolution, by a Dicomed D-48 color film recorder, controlled by a Varian V-75 minicomputer. The Varian computes the shading and highlights for each pixel in a fast microcoded loop. Recent modifications to give shadows and transparency are described.

High resolution color raster computer animation of space filling molecular models

International Nuclear Information System (INIS)

Max, N.L.

1981-01-01

The ATOMLLL system efficiently produces realistic photographs of ball-and-stick or space-filling molecular models, with color shading, highlights, shadows, and transparency. The hidden surface problem for a scene composed of intersecting spheres and cylinders is solved on a CDC-7600, which outputs onto magnetic tape the outlines of the visible parts of each object. The outlines are then rendered, at up to 4096 x 4096 resolution, by a Dicomed D-48 color film recorder, controlled by a Varian V-75 minicomputer. The Varian computes the shading and highlights for each pixel in a fast microcoded loop. Recent modifications to give shadows and transparency are described

The effect of a realistic thermal diffusivity on numerical model of a subducting slab

Science.gov (United States)

Maierova, P.; Steinle-Neumann, G.; Cadek, O.

2010-12-01

A number of numerical studies of subducting slab assume simplified (constant or only depth-dependent) models of thermal conductivity. The available mineral physics data indicate, however, that thermal diffusivity is strongly temperature- and pressure-dependent and may also vary among different mantle materials. In the present study, we examine the influence of realistic thermal properties of mantle materials on the thermal state of the upper mantle and the dynamics of subducting slabs. On the basis of the data published in mineral physics literature we compile analytical relationships that approximate the pressure and temperature dependence of thermal diffusivity for major mineral phases of the mantle (olivine, wadsleyite, ringwoodite, garnet, clinopyroxenes, stishovite and perovskite). We propose a simplified composition of mineral assemblages predominating in the subducting slab and the surrounding mantle (pyrolite, mid-ocean ridge basalt, harzburgite) and we estimate their thermal diffusivity using the Hashin-Shtrikman bounds. The resulting complex formula for the diffusivity of each aggregate is then approximated by a simpler analytical relationship that is used in our numerical model as an input parameter. For the numerical modeling we use the Elmer software (open source finite element software for multiphysical problems, see http://www.csc.fi/english/pages/elmer). We set up a 2D Cartesian thermo-mechanical steady-state model of a subducting slab. The model is partly kinematic as the flow is driven by a boundary condition on velocity that is prescribed on the top of the subducting lithospheric plate. Reology of the material is non-linear and is coupled with the thermal equation. Using the realistic relationship for thermal diffusivity of mantle materials, we compute the thermal and flow fields for different input velocity and age of the subducting plate and we compare the results against the models assuming a constant thermal diffusivity. The importance of the

More Realistic Face Model Surface Improves Relevance of Pediatric In-Vitro Aerosol Studies.

Science.gov (United States)

Amirav, Israel; Halamish, Asaf; Gorenberg, Miguel; Omar, Hamza; Newhouse, Michael T

2015-01-01

Various hard face models are commonly used to evaluate the efficiency of aerosol face masks. Softer more realistic "face" surface materials, like skin, deform upon mask application and should provide more relevant in-vitro tests. Studies that simultaneously take into consideration many of the factors characteristic of the in vivo face are lacking. These include airways, various application forces, comparison of various devices, comparison with a hard-surface model and use of a more representative model face based on large numbers of actual faces. To compare mask to "face" seal and aerosol delivery of two pediatric masks using a soft vs. a hard, appropriately representative, pediatric face model under various applied forces. Two identical face models and upper airways replicas were constructed, the only difference being the suppleness and compressibility of the surface layer of the "face." Integrity of the seal and aerosol delivery of two different masks [AeroChamber (AC) and SootherMask (SM)] were compared using a breath simulator, filter collection and realistic applied forces. The soft "face" significantly increased the delivery efficiency and the sealing characteristics of both masks. Aerosol delivery with the soft "face" was significantly greater for the SM compared to the AC (pmasks was observed with the hard "face." The material and pliability of the model "face" surface has a significant influence on both the seal and delivery efficiency of face masks. This finding should be taken into account during in-vitro aerosol studies.

Characterization of photomultiplier tubes with a realistic model through GPU-boosted simulation

Science.gov (United States)

Anthony, M.; Aprile, E.; Grandi, L.; Lin, Q.; Saldanha, R.

2018-02-01

The accurate characterization of a photomultiplier tube (PMT) is crucial in a wide-variety of applications. However, current methods do not give fully accurate representations of the response of a PMT, especially at very low light levels. In this work, we present a new and more realistic model of the response of a PMT, called the cascade model, and use it to characterize two different PMTs at various voltages and light levels. The cascade model is shown to outperform the more common Gaussian model in almost all circumstances and to agree well with a newly introduced model independent approach. The technical and computational challenges of this model are also presented along with the employed solution of developing a robust GPU-based analysis framework for this and other non-analytical models.

Convective aggregation in idealised models and realistic equatorial cases

Science.gov (United States)

Holloway, Chris

2015-04-01

Idealised explicit convection simulations of the Met Office Unified Model are shown to exhibit spontaneous self-aggregation in radiative-convective equilibrium, as seen previously in other models in several recent studies. This self-aggregation is linked to feedbacks between radiation, surface fluxes, and convection, and the organization is intimately related to the evolution of the column water vapour (CWV) field. To investigate the relevance of this behaviour to the real world, these idealized simulations are compared with five 15-day cases of real organized convection in the tropics, including multiple simulations of each case testing sensitivities of the convective organization and mean states to interactive radiation, interactive surface fluxes, and evaporation of rain. Despite similar large-scale forcing via lateral boundary conditions, systematic differences in mean CWV, CWV distribution shape, and the length scale of CWV features are found between the different sensitivity runs, showing that there are at least some similarities in sensitivities to these feedbacks in both idealized and realistic simulations.

A COMPARISON OF METHODS FOR DETERMINING THE MOLECULAR CONTENT OF MODEL GALAXIES

International Nuclear Information System (INIS)

Krumholz, Mark R.; Gnedin, Nickolay Y.

2011-01-01

Recent observations indicate that star formation occurs only in the molecular phase of a galaxy's interstellar medium. A realistic treatment of star formation in simulations and analytic models of galaxies therefore requires that one determine where the transition from the atomic to molecular gas occurs. In this paper, we compare two methods for making this determination in cosmological simulations where the internal structures of molecular clouds are unresolved: a complex time-dependent chemistry network coupled to a radiative transfer calculation of the dissociating ultraviolet (UV) radiation field and a simple time-independent analytic approximation. We show that these two methods produce excellent agreement at all metallicities ∼>10 -2 of the Milky Way value across a very wide range of UV fields. At lower metallicities the agreement is worse, likely because time-dependent effects become important; however, there are no observational calibrations of molecular gas content at such low metallicities, so it is unclear if either method is accurate. The comparison suggests that, in many but not all applications, the analytic approximation provides a viable and nearly cost-free alternative to full time-dependent chemistry and radiative transfer.

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

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

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

The Realistic Versus the Spherical Head Model in EEG Dipole Source Analysis in the Presence of Noise

National Research Council Canada - National Science Library

Vanrumste, Bart

2001-01-01

.... For 27 electrodes, an EEG epoch of one time sample and spatially white Gaussian noise we found that the importance of the realistic head model over the spherical head model reduces by increasing the noise level.

Problem Posing with Realistic Mathematics Education Approach in Geometry Learning

Science.gov (United States)

Mahendra, R.; Slamet, I.; Budiyono

2017-09-01

One of the difficulties of students in the learning of geometry is on the subject of plane that requires students to understand the abstract matter. The aim of this research is to determine the effect of Problem Posing learning model with Realistic Mathematics Education Approach in geometry learning. This quasi experimental research was conducted in one of the junior high schools in Karanganyar, Indonesia. The sample was taken using stratified cluster random sampling technique. The results of this research indicate that the model of Problem Posing learning with Realistic Mathematics Education Approach can improve students’ conceptual understanding significantly in geometry learning especially on plane topics. It is because students on the application of Problem Posing with Realistic Mathematics Education Approach are become to be active in constructing their knowledge, proposing, and problem solving in realistic, so it easier for students to understand concepts and solve the problems. Therefore, the model of Problem Posing learning with Realistic Mathematics Education Approach is appropriately applied in mathematics learning especially on geometry material. Furthermore, the impact can improve student achievement.

A realistic extension of gauge-mediated SUSY-breaking model with superconformal hidden sector

International Nuclear Information System (INIS)

Asano, Masaki; Hisano, Junji; Okada, Takashi; Sugiyama, Shohei

2009-01-01

The sequestering of supersymmetry (SUSY) breaking parameters, which is induced by superconformal hidden sector, is one of the solutions for the μ/B μ problem in gauge-mediated SUSY-breaking scenario. However, it is found that the minimal messenger model does not derive the correct electroweak symmetry breaking. In this Letter we present a model which has the coupling of the messengers with the SO(10) GUT-symmetry breaking Higgs fields. The model is one of the realistic extensions of the gauge mediation model with superconformal hidden sector. It is shown that the extension is applicable for a broad range of conformality breaking scale

An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

Directory of Open Access Journals (Sweden)

Matthew W. Thompson

2017-10-01

Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

Molecular Modeling

Indian Academy of Sciences (India)

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

Comparative study of non-premixed and partially-premixed combustion simulations in a realistic Tay model combustor

OpenAIRE

Zhang, K.; Ghobadian, A.; Nouri, J. M.

2017-01-01

A comparative study of two combustion models based on non-premixed assumption and partially premixed assumptions using the overall models of Zimont Turbulent Flame Speed Closure Method (ZTFSC) and Extended Coherent Flamelet Method (ECFM) are conducted through Reynolds stress turbulence modelling of Tay model gas turbine combustor for the first time. The Tay model combustor retains all essential features of a realistic gas turbine combustor. It is seen that the non-premixed combustion model fa...

Modeling the Earth's magnetospheric magnetic field confined within a realistic magnetopause

Science.gov (United States)

Tsyganenko, N. A.

1995-01-01

Empirical data-based models of the magnetosphereic magnetic field have been widely used during recent years. However, the existing models (Tsyganenko, 1987, 1989a) have three serious deficiencies: (1) an unstable de facto magnetopause, (2) a crude parametrization by the K(sub p) index, and (3) inaccuracies in the equatorial magnetotail B(sub z) values. This paper describes a new approach to the problem; the essential new features are (1) a realistic shape and size of the magnetopause, based on fits to a large number of observed crossing (allowing a parametrization by the solar wind pressure), (2) fully controlled shielding of the magnetic field produced by all magnetospheric current systems, (3) new flexible representations for the tail and ring currents, and (4) a new directional criterion for fitting the model field to spacecraft data, providing improved accuracy for field line mapping. Results are presented from initial efforts to create models assembled from these modules and calibrated against spacecraft data sets.

Novel high-fidelity realistic explosion damage simulation for urban environments

Science.gov (United States)

Liu, Xiaoqing; Yadegar, Jacob; Zhu, Youding; Raju, Chaitanya; Bhagavathula, Jaya

2010-04-01

Realistic building damage simulation has a significant impact in modern modeling and simulation systems especially in diverse panoply of military and civil applications where these simulation systems are widely used for personnel training, critical mission planning, disaster management, etc. Realistic building damage simulation should incorporate accurate physics-based explosion models, rubble generation, rubble flyout, and interactions between flying rubble and their surrounding entities. However, none of the existing building damage simulation systems sufficiently faithfully realize the criteria of realism required for effective military applications. In this paper, we present a novel physics-based high-fidelity and runtime efficient explosion simulation system to realistically simulate destruction to buildings. In the proposed system, a family of novel blast models is applied to accurately and realistically simulate explosions based on static and/or dynamic detonation conditions. The system also takes account of rubble pile formation and applies a generic and scalable multi-component based object representation to describe scene entities and highly scalable agent-subsumption architecture and scheduler to schedule clusters of sequential and parallel events. The proposed system utilizes a highly efficient and scalable tetrahedral decomposition approach to realistically simulate rubble formation. Experimental results demonstrate that the proposed system has the capability to realistically simulate rubble generation, rubble flyout and their primary and secondary impacts on surrounding objects including buildings, constructions, vehicles and pedestrians in clusters of sequential and parallel damage events.

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.

3D realistic head model simulation based on transcranial magnetic stimulation.

Science.gov (United States)

Yang, Shuo; Xu, Guizhi; Wang, Lei; Chen, Yong; Wu, Huanli; Li, Ying; Yang, Qingxin

2006-01-01

Transcranial magnetic stimulation (TMS) is a powerful non-invasive tool for investigating functions in the brain. The target inside the head is stimulated with eddy currents induced in the tissue by the time-varying magnetic field. Precise spatial localization of stimulation sites is the key of efficient functional magnetic stimulations. Many researchers devote to magnetic field analysis in empty free space. In this paper, a realistic head model used in Finite Element Method has been developed. The magnetic field inducted in the head bt TMS has been analysed. This three-dimensional simulation is useful for spatial localization of stimulation.

Evaluation of photovoltaic panel temperature in realistic scenarios

International Nuclear Information System (INIS)

Du, Yanping; Fell, Christopher J.; Duck, Benjamin; Chen, Dong; Liffman, Kurt; Zhang, Yinan; Gu, Min; Zhu, Yonggang

2016-01-01

Highlights: • The developed realistic model captures more reasonably the thermal response and hysteresis effects. • The predicted panel temperature is as high as 60 °C under a solar irradiance of 1000 W/m"2 in no-wind weather. • In realistic scenarios, the thermal response normally takes 50–250 s. • The actual heating effect may cause a photoelectric efficiency drop of 2.9–9.0%. - Abstract: Photovoltaic (PV) panel temperature was evaluated by developing theoretical models that are feasible to be used in realistic scenarios. Effects of solar irradiance, wind speed and ambient temperature on the PV panel temperature were studied. The parametric study shows significant influence of solar irradiance and wind speed on the PV panel temperature. With an increase of ambient temperature, the temperature rise of solar cells is reduced. The characteristics of panel temperature in realistic scenarios were analyzed. In steady weather conditions, the thermal response time of a solar cell with a Si thickness of 100–500 μm is around 50–250 s. While in realistic scenarios, the panel temperature variation in a day is different from that in steady weather conditions due to the effect of thermal hysteresis. The heating effect on the photovoltaic efficiency was assessed based on real-time temperature measurement of solar cells in realistic weather conditions. For solar cells with a temperature coefficient in the range of −0.21%∼−0.50%, the current field tests indicated an approximate efficiency loss between 2.9% and 9.0%.

Simple and Realistic Data Generation

DEFF Research Database (Denmark)

Pedersen, Kenneth Houkjær; Torp, Kristian; Wind, Rico

2006-01-01

This paper presents a generic, DBMS independent, and highly extensible relational data generation tool. The tool can efficiently generate realistic test data for OLTP, OLAP, and data streaming applications. The tool uses a graph model to direct the data generation. This model makes it very simple...... to generate data even for large database schemas with complex inter- and intra table relationships. The model also makes it possible to generate data with very accurate characteristics....

The discussion of descriptors for the QSAR model and molecular dynamics simulation of benzimidazole derivatives as corrosion inhibitors

International Nuclear Information System (INIS)

Li, Lu; Zhang, Xiuhui; Gong, Shida; Zhao, Hongxia; Bai, Yang; Li, Qianshu; Ji, Lin

2015-01-01

Graphical abstract: - Highlights: • Aromaticity is used as a descriptor in QSAR model to describe corrosion inhibition. • Improved calculation of I and A is correlated well with inhibition efficiencies. • Binding energies were calculated using a realistic corrosion environment. • Nonlinear QSAR model was built by support vector machine with radial basis function. • Six designed benzimidazole molecules are predicted with high inhibition efficiencies. - Abstract: The corrosion inhibition performances of 20 protonated benzimidazole derivatives were studied using theoretical methods. Nuclear Independent Chemical Shift (NICS), the measurement of aromaticity, demonstrated good correlation with inhibition efficiencies and was used as a descriptor. Binding energies were calculated on the basis of molecular dynamics simulations using a realistic corrosive environment. Some improved descriptors correlate well with experimental inhibition efficiencies. A reliable nonlinear quantitative structure–activity relationship model was constructed by a support vector machine approach. The correlation coefficient and root-mean-square error were 0.96 and 6.79%, respectively. Additionally, six new benzimidazole molecules were designed, and their inhibition efficiencies were predicted.

Bending and Twisting the Embryonic Heart: A Computational Model for C-Looping Based on Realistic Geometry

Directory of Open Access Journals (Sweden)

Yunfei eShi

2014-08-01

Full Text Available The morphogenetic process of cardiac looping transforms the straight heart tube into a curved tube that resembles the shape of the future four-chambered heart. Although great progress has been made in identifying the molecular and genetic factors involved in looping, the physical mechanisms that drive this process have remained poorly understood. Recent work, however, has shed new light on this complicated problem. After briefly reviewing the current state of knowledge, we propose a relatively comprehensive hypothesis for the mechanics of the first phase of looping, termed c-looping, as the straight heart tube deforms into a c-shaped tube. According to this hypothesis, differential hypertrophic growth in the myocardium supplies the main forces that cause the heart tube to bend ventrally, while regional growth and contraction in the omphalomesenteric veins (primitive atria and compressive loads exerted by the splanchnopleuric membrane drive rightward torsion. A computational model based on realistic embryonic heart geometry is used to test this hypothesis. The behavior of the model is in reasonable agreement with available experimental data from control and perturbed embryos, offering support for our hypothesis. The results also suggest, however, that several other mechanisms contribute secondarily to normal looping, and we speculate that these mechanisms play backup roles when looping is perturbed. Finally, some outstanding questions are discussed for future study.

Use of realistic anthropomorphic models for calculation of radiation dose in nuclear medicine

International Nuclear Information System (INIS)

Stabin, Michael G.; Emmons, Mary A.; Fernald, Michael J.; Brill, A.B.; Segars, W.Paul

2008-01-01

Anthropomorphic phantoms based on simple geometric structures have been used in radiation dose calculations for many years. We have now developed a series of anatomically realistic phantoms representing adults and children using body models based on non-uniform rational B-spline (NURBS), with organ and body masses based on the reference values given in ICRP Publication 89. Age-dependent models were scaled and shaped to represent the reference individuals described in ICRP 89 (male and female adults, newborns, 1-, 5-, 10- and 15-year-olds), using a software tool developed in Visual C++. Voxel-based versions of these models were used with GEANT4 radiation transport codes for calculation of specific absorbed fractions (SAFs) for internal sources of photons and electrons, using standard starting energy values. Organ masses in the models were within a few % of ICRP reference masses, and physicians reviewed the models for anatomical realism. Development of individual phantoms was much faster than manual segmentation of medical images, and resulted in a very uniform standardized phantom series. SAFs were calculated on the Vanderbilt multi node computing network (ACCRE). Photon and electron SAFs were calculated for all organs in all models, and were compared to values from similar phantoms developed by others. Agreement was very good in most cases; some differences were seen, due to differences in organ mass and geometry. This realistic phantom series represents a possible replacement for the Cristy/Eckerman series of the 1980's. Both phantom sets will be included in the next release of the OLINDA/EXM personal computer code, and the new phantoms will be made generally available to the research community for other uses. Calculated radiation doses for diagnostic and therapeutic radiopharmaceuticals will be compared with previous values. (author)

Realistic Noise Assessment and Strain Analysis of Iranian Permanent GPS Stations

Science.gov (United States)

Razeghi, S. M.; Amiri Simkooei, A. A.; Sharifi, M. A.

2012-04-01

To assess noise characteristics of Iranian Permanent GPS Stations (IPGS), northwestern part of this network namely Azerbaijan Continuous GPS Station (ACGS), was selected. For a realistic noise assessment it is required to model all deterministic signals of the GPS time series by means of least squares harmonic estimation (LS-HE) and derive all periodic behavior of the series. After taking all deterministic signals into account, the least squares variance component estimation (LS-VCE) is used to obtain a realistic noise model (white noise plus flicker noise) of the ACGS. For this purpose, one needs simultaneous GPS time series for which a multivariate noise assessment is applied. Having determined realistic noise model, a realistic strain analysis of the network is obtained for which one relies on the finite element methods. Finite element is now considered to be a new functional model and the new stochastic model is given based on the multivariate noise assessment using LS-VCE. The deformation rates of the components along with their full covariance matries are input to the strain analysis. Further, the results are also provided using a pure white noise model. The normalized strains for these two models show that the strain parameters derived from a realistic noise model are less significant than those derived from the white model. This could be either due to the short time span of the time series used or due to the intrinsic behavior of the strain parameters in the ACGS. Longer time series are required to further elaborate this issue.

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.

Robust mode space approach for atomistic modeling of realistically large nanowire transistors

Science.gov (United States)

Huang, Jun Z.; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

2018-01-01

Nanoelectronic transistors have reached 3D length scales in which the number of atoms is countable. Truly atomistic device representations are needed to capture the essential functionalities of the devices. Atomistic quantum transport simulations of realistically extended devices are, however, computationally very demanding. The widely used mode space (MS) approach can significantly reduce the numerical cost, but a good MS basis is usually very hard to obtain for atomistic full-band models. In this work, a robust and parallel algorithm is developed to optimize the MS basis for atomistic nanowires. This enables engineering-level, reliable tight binding non-equilibrium Green's function simulation of nanowire metal-oxide-semiconductor field-effect transistor (MOSFET) with a realistic cross section of 10 nm × 10 nm using a small computer cluster. This approach is applied to compare the performance of InGaAs and Si nanowire n-type MOSFETs (nMOSFETs) with various channel lengths and cross sections. Simulation results with full-band accuracy indicate that InGaAs nanowire nMOSFETs have no drive current advantage over their Si counterparts for cross sections up to about 10 nm × 10 nm.

A Radiosity Approach to Realistic Image Synthesis

Science.gov (United States)

1992-12-01

AD-A259 082 AFIT/GCE/ENG/92D-09 A RADIOSITY APPROACH TO REALISTIC IMAGE SYNTHESIS THESIS Richard L. Remington Captain, USAF fl ECTE AFIT/GCE/ENG/92D...09 SJANl 1993U 93-00134 Approved for public release; distribution unlimited 93& 1! A -A- AFIT/GCE/ENG/92D-09 A RADIOSITY APPROACH TO REALISTIC IMAGE...assistance in creating the input geometry file for the AWACS aircraft interior. Without his assistance, a good model for the diffuse radiosity implementation

Electron distribution in polar heterojunctions within a realistic model

Energy Technology Data Exchange (ETDEWEB)

Tien, Nguyen Thanh, E-mail: thanhtienctu@gmail.com [College of Natural Science, Can Tho University, 3-2 Road, Can Tho City (Viet Nam); Thao, Dinh Nhu [Center for Theoretical and Computational Physics, College of Education, Hue University, 34 Le Loi Street, Hue City (Viet Nam); Thao, Pham Thi Bich [College of Natural Science, Can Tho University, 3-2 Road, Can Tho City (Viet Nam); Quang, Doan Nhat [Institute of Physics, Vietnamese Academy of Science and Technology, 10 Dao Tan Street, Hanoi (Viet Nam)

2015-12-15

We present a theoretical study of the electron distribution, i.e., two-dimensional electron gas (2DEG) in polar heterojunctions (HJs) within a realistic model. The 2DEG is confined along the growth direction by a triangular quantum well with a finite potential barrier and a bent band figured by all confinement sources. Therein, interface polarization charges take a double role: they induce a confining potential and, furthermore, they can make some change in other confinements, e.g., in the Hartree potential from ionized impurities and 2DEG. Confinement by positive interface polarization charges is necessary for the ground state of 2DEG existing at a high sheet density. The 2DEG bulk density is found to be increased in the barrier, so that the scattering occurring in this layer (from interface polarization charges and alloy disorder) becomes paramount in a polar modulation-doped HJ.

Magnetic reconnection in the low solar chromosphere with a more realistic radiative cooling model

Science.gov (United States)

Ni, Lei; Lukin, Vyacheslav S.; Murphy, Nicholas A.; Lin, Jun

2018-04-01

Magnetic reconnection is the most likely mechanism responsible for the high temperature events that are observed in strongly magnetized locations around the temperature minimum in the low solar chromosphere. This work improves upon our previous work [Ni et al., Astrophys. J. 852, 95 (2018)] by using a more realistic radiative cooling model computed from the OPACITY project and the CHIANTI database. We find that the rate of ionization of the neutral component of the plasma is still faster than recombination within the current sheet region. For low β plasmas, the ionized and neutral fluid flows are well-coupled throughout the reconnection region resembling the single-fluid Sweet-Parker model dynamics. Decoupling of the ion and neutral inflows appears in the higher β case with β0=1.46 , which leads to a reconnection rate about three times faster than the rate predicted by the Sweet-Parker model. In all cases, the plasma temperature increases with time inside the current sheet, and the maximum value is above 2 ×104 K when the reconnection magnetic field strength is greater than 500 G. While the more realistic radiative cooling model does not result in qualitative changes of the characteristics of magnetic reconnection, it is necessary for studying the variations of the plasma temperature and ionization fraction inside current sheets in strongly magnetized regions of the low solar atmosphere. It is also important for studying energy conversion during the magnetic reconnection process when the hydrogen-dominated plasma approaches full ionization.

Hemodynamic Changes Caused by Flow Diverters in Rabbit Aneurysm Models: Comparison of Virtual and Realistic FD Deployments Based on Micro-CT Reconstruction

Science.gov (United States)

Fang, Yibin; Yu, Ying; Cheng, Jiyong; Wang, Shengzhang; Wang, Kuizhong; Liu, Jian-Min; Huang, Qinghai

2013-01-01

Adjusting hemodynamics via flow diverter (FD) implantation is emerging as a novel method of treating cerebral aneurysms. However, most previous FD-related hemodynamic studies were based on virtual FD deployment, which may produce different hemodynamic outcomes than realistic (in vivo) FD deployment. We compared hemodynamics between virtual FD and realistic FD deployments in rabbit aneurysm models using computational fluid dynamics (CFD) simulations. FDs were implanted for aneurysms in 14 rabbits. Vascular models based on rabbit-specific angiograms were reconstructed for CFD studies. Real FD configurations were reconstructed based on micro-CT scans after sacrifice, while virtual FD configurations were constructed with SolidWorks software. Hemodynamic parameters before and after FD deployment were analyzed. According to the metal coverage (MC) of implanted FDs calculated based on micro-CT reconstruction, 14 rabbits were divided into two groups (A, MC >35%; B, MC 0.05). The normalized mean WSS in Group A after realistic FD implantation was significantly lower than that of Group B. All parameters in Group B exhibited no significant difference between realistic and virtual FDs. This study confirmed MC-correlated differences in hemodynamic parameters between realistic and virtual FD deployment. PMID:23823503

Triangulating and guarding realistic polygons

NARCIS (Netherlands)

Aloupis, G.; Bose, P.; Dujmovic, V.; Gray, C.M.; Langerman, S.; Speckmann, B.

2008-01-01

We propose a new model of realistic input: k-guardable objects. An object is k-guardable if its boundary can be seen by k guards in the interior of the object. In this abstract, we describe a simple algorithm for triangulating k-guardable polygons. Our algorithm, which is easily implementable, takes

Molecular Modelling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-12-01

Full Text Available

Realistic full wave modeling of focal plane array pixels.

Energy Technology Data Exchange (ETDEWEB)

Campione, Salvatore [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Warne, Larry K. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Jorgenson, Roy E. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Electromagnetic Theory Dept.; Davids, Paul [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Applied Photonic Microsystems Dept.; Peters, David W. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States). Applied Photonic Microsystems Dept.

2017-11-01

Here, we investigate full-wave simulations of realistic implementations of multifunctional nanoantenna enabled detectors (NEDs). We focus on a 2x2 pixelated array structure that supports two wavelengths of operation. We design each resonating structure independently using full-wave simulations with periodic boundary conditions mimicking the whole infinite array. We then construct a supercell made of a 2x2 pixelated array with periodic boundary conditions mimicking the full NED; in this case, however, each pixel comprises 10-20 antennas per side. In this way, the cross-talk between contiguous pixels is accounted for in our simulations. We observe that, even though there are finite extent effects, the pixels work as designed, each responding at the respective wavelength of operation. This allows us to stress that realistic simulations of multifunctional NEDs need to be performed to verify the design functionality by taking into account finite extent and cross-talk effects.

Improved transcranial magnetic stimulation coil design with realistic head modeling

Science.gov (United States)

Crowther, Lawrence; Hadimani, Ravi; Jiles, David

2013-03-01

We are investigating Transcranial magnetic stimulation (TMS) as a noninvasive technique based on electromagnetic induction which causes stimulation of the neurons in the brain. TMS can be used as a pain-free alternative to conventional electroconvulsive therapy (ECT) which is still widely implemented for treatment of major depression. Development of improved TMS coils capable of stimulating subcortical regions could also allow TMS to replace invasive deep brain stimulation (DBS) which requires surgical implantation of electrodes in the brain. Our new designs allow new applications of the technique to be established for a variety of diagnostic and therapeutic applications of psychiatric disorders and neurological diseases. Calculation of the fields generated inside the head is vital for the use of this method for treatment. In prior work we have implemented a realistic head model, incorporating inhomogeneous tissue structures and electrical conductivities, allowing the site of neuronal activation to be accurately calculated. We will show how we utilize this model in the development of novel TMS coil designs to improve the depth of penetration and localization of stimulation produced by stimulator coils.

Automatic skull segmentation from MR images for realistic volume conductor models of the head: Assessment of the state-of-the-art

DEFF Research Database (Denmark)

Nielsen, Jesper Duemose; Madsen, Kristoffer Hougaard; Puonti, Oula

2018-01-01

Anatomically realistic volume conductor models of the human head are important for accurate forward modeling of the electric field during transcranial brain stimulation (TBS), electro- (EEG) and magnetoencephalography (MEG). In particular, the skull compartment exerts a strong influence on the fi......Anatomically realistic volume conductor models of the human head are important for accurate forward modeling of the electric field during transcranial brain stimulation (TBS), electro- (EEG) and magnetoencephalography (MEG). In particular, the skull compartment exerts a strong influence...... local defects. In contrast to FSL BET2, the SPM12-based segmentation with extended spatial tissue priors and the BrainSuite-based segmentation provide coarse reconstructions of the vertebrae, enabling the construction of volume conductor models that include the neck. We exemplarily demonstrate...

RenderGAN: Generating Realistic Labeled Data

Directory of Open Access Journals (Sweden)

Leon Sixt

2018-06-01

Full Text Available Deep Convolutional Neuronal Networks (DCNNs are showing remarkable performance on many computer vision tasks. Due to their large parameter space, they require many labeled samples when trained in a supervised setting. The costs of annotating data manually can render the use of DCNNs infeasible. We present a novel framework called RenderGAN that can generate large amounts of realistic, labeled images by combining a 3D model and the Generative Adversarial Network framework. In our approach, image augmentations (e.g., lighting, background, and detail are learned from unlabeled data such that the generated images are strikingly realistic while preserving the labels known from the 3D model. We apply the RenderGAN framework to generate images of barcode-like markers that are attached to honeybees. Training a DCNN on data generated by the RenderGAN yields considerably better performance than training it on various baselines.

A Local-Realistic Model of Quantum Mechanics Based on a Discrete Spacetime

Science.gov (United States)

Sciarretta, Antonio

2018-01-01

This paper presents a realistic, stochastic, and local model that reproduces nonrelativistic quantum mechanics (QM) results without using its mathematical formulation. The proposed model only uses integer-valued quantities and operations on probabilities, in particular assuming a discrete spacetime under the form of a Euclidean lattice. Individual (spinless) particle trajectories are described as random walks. Transition probabilities are simple functions of a few quantities that are either randomly associated to the particles during their preparation, or stored in the lattice nodes they visit during the walk. QM predictions are retrieved as probability distributions of similarly-prepared ensembles of particles. The scenarios considered to assess the model comprise of free particle, constant external force, harmonic oscillator, particle in a box, the Delta potential, particle on a ring, particle on a sphere and include quantization of energy levels and angular momentum, as well as momentum entanglement.

EIT forward problem parallel simulation environment with anisotropic tissue and realistic electrode models.

Science.gov (United States)

De Marco, Tommaso; Ries, Florian; Guermandi, Marco; Guerrieri, Roberto

2012-05-01

Electrical impedance tomography (EIT) is an imaging technology based on impedance measurements. To retrieve meaningful insights from these measurements, EIT relies on detailed knowledge of the underlying electrical properties of the body. This is obtained from numerical models of current flows therein. The nonhomogeneous and anisotropic electric properties of human tissues make accurate modeling and simulation very challenging, leading to a tradeoff between physical accuracy and technical feasibility, which at present severely limits the capabilities of EIT. This work presents a complete algorithmic flow for an accurate EIT modeling environment featuring high anatomical fidelity with a spatial resolution equal to that provided by an MRI and a novel realistic complete electrode model implementation. At the same time, we demonstrate that current graphics processing unit (GPU)-based platforms provide enough computational power that a domain discretized with five million voxels can be numerically modeled in about 30 s.

Polarization effects in molecular mechanical force fields

Energy Technology Data Exchange (ETDEWEB)

Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

2009-08-19

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

Computation of Surface Laplacian for tri-polar ring electrodes on high-density realistic geometry head model.

Science.gov (United States)

Junwei Ma; Han Yuan; Sunderam, Sridhar; Besio, Walter; Lei Ding

2017-07-01

Neural activity inside the human brain generate electrical signals that can be detected on the scalp. Electroencephalograph (EEG) is one of the most widely utilized techniques helping physicians and researchers to diagnose and understand various brain diseases. Due to its nature, EEG signals have very high temporal resolution but poor spatial resolution. To achieve higher spatial resolution, a novel tri-polar concentric ring electrode (TCRE) has been developed to directly measure Surface Laplacian (SL). The objective of the present study is to accurately calculate SL for TCRE based on a realistic geometry head model. A locally dense mesh was proposed to represent the head surface, where the local dense parts were to match the small structural components in TCRE. Other areas without dense mesh were used for the purpose of reducing computational load. We conducted computer simulations to evaluate the performance of the proposed mesh and evaluated possible numerical errors as compared with a low-density model. Finally, with achieved accuracy, we presented the computed forward lead field of SL for TCRE for the first time in a realistic geometry head model and demonstrated that it has better spatial resolution than computed SL from classic EEG recordings.

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.

Magnetohydrodynamic Models of Molecular Tornadoes

Energy Technology Data Exchange (ETDEWEB)

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

2017-07-10

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

A Madden-Julian oscillation event realistically simulated by a global cloud-resolving model.

Science.gov (United States)

Miura, Hiroaki; Satoh, Masaki; Nasuno, Tomoe; Noda, Akira T; Oouchi, Kazuyoshi

2007-12-14

A Madden-Julian Oscillation (MJO) is a massive weather event consisting of deep convection coupled with atmospheric circulation, moving slowly eastward over the Indian and Pacific Oceans. Despite its enormous influence on many weather and climate systems worldwide, it has proven very difficult to simulate an MJO because of assumptions about cumulus clouds in global meteorological models. Using a model that allows direct coupling of the atmospheric circulation and clouds, we successfully simulated the slow eastward migration of an MJO event. Topography, the zonal sea surface temperature gradient, and interplay between eastward- and westward-propagating signals controlled the timing of the eastward transition of the convective center. Our results demonstrate the potential making of month-long MJO predictions when global cloud-resolving models with realistic initial conditions are used.

Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene

Directory of Open Access Journals (Sweden)

Kubicki JD

2000-09-01

Full Text Available Molecular simulations (energy minimizations and molecular dynamics of an n-hexane soot model developed by Smith and co-workers (M. S. Akhter, A. R. Chughtai and D. M. Smith, Appl. Spectrosc., 1985, 39, 143; ref. 1 were performed. The MM+ (N. L. Allinger, J. Am. Chem. Soc., 1977, 395, 157; ref. 2 and COMPASS (H. Sun, J. Phys. Chem., 1998, 102, 7338; ref. 3 force fields were tested for their ability to produce realistic soot nanoparticle structure. The interaction of pyrene with the model soot was simulated. Quantum mechanical calculations on smaller soot fragments were carried out. Starting from an initial 2D structure, energy minimizations are not able to produce the observed layering within soot with either force field. Results of molecular dynamics simulations indicate that the COMPASS force field does a reasonably accurate job of reproducing observations of soot structure. Increasing the system size from a 683 to a 2732 atom soot model does not have a significant effect on predicted structures. Neither does the addition of water molecules surrounding the soot model. Pyrene fits within the soot structure without disrupting the interlayer spacing. Polycyclic aromatic hydrocarbons (PAH, such as pyrene, may strongly partition into soot and have slow desorption kinetics because the PAH-soot bonding is similar to soot–soot interactions. Diffusion of PAH into soot micropores may allow the PAH to be irreversibly adsorbed and sequestered so that they partition slowly back into an aqueous phase causing dis-equilibrium between soil organic matter and porewater.

Regional 3-D Modeling of Ground Geoelectric Field for the Northeast United States due to Realistic Geomagnetic Disturbances

Science.gov (United States)

Ivannikova, E.; Kruglyakov, M.; Kuvshinov, A. V.; Rastaetter, L.; Pulkkinen, A. A.; Ngwira, C. M.

2017-12-01

During extreme space weather events electric currents in the Earth's magnetosphere and ionosphere experience large variations, which leads to dramatic intensification of the fluctuating magnetic field at the surface of the Earth. According to Faraday's law of induction, the fluctuating geomagnetic field in turn induces electric field that generates harmful currents (so-called "geomagnetically induced currents"; GICs) in grounded technological systems. Understanding (via modeling) of the spatio-temporal evolution of the geoelectric field during enhanced geomagnetic activity is a key consideration in estimating the hazard to technological systems from space weather. We present the results of ground geoelectric field modeling for the Northeast United States, which is performed with the use of our novel numerical tool based on integral equation approach. The tool exploits realistic regional three-dimensional (3-D) models of the Earth's electrical conductivity and realistic global models of the spatio-temporal evolution of the magnetospheric and ionospheric current systems responsible for geomagnetic disturbances. We also explore in detail the manifestation of the coastal effect (anomalous intensification of the geoelectric field near the coasts) in this region.

Molecular Simulation Results on Charged Carbon Nanotube Forest-Based Supercapacitors.

Science.gov (United States)

Muralidharan, Ajay; Pratt, Lawrence R; Hoffman, Gary G; Chaudhari, Mangesh I; Rempe, Susan B

2018-05-03

Electrochemical double-layer capacitances of charged carbon nanotube (CNT) forests with tetraethyl ammonium tetrafluoro borate electrolyte in propylene carbonate are studied on the basis of molecular dynamics simulation. Direct molecular simulation of the filling of pore spaces of the forest is feasible even with realistic, small CNT spacings. The numerical solution of the Poisson equation based on the extracted average charge densities then yields a regular experimental dependence on the width of the pore spaces, in contrast to the anomalous pattern observed in experiments on other carbon materials and also in simulations on planar slot-like pores. The capacitances obtained have realistic magnitudes but are insensitive to electric potential differences between the electrodes in this model. This agrees with previous calculations on CNT forest supercapacitors, but not with experiments which have suggested electrochemical doping for these systems. Those phenomena remain for further theory/modeling work. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A realistic approach to modeling an in-duct desulfurization process based on an experimental pilot plant study

Energy Technology Data Exchange (ETDEWEB)

Ortiz, F.J.G.; Ollero, P. [University of Seville, Seville (Spain)

2008-07-15

This paper has been written to provide a realistic approach to modeling an in-duct desulfurization process and because of the disagreement between the results predicted by published kinetic models of the reaction between hydrated lime and SO{sub 2} at low temperature and the experimental results obtained in pilot plants where this process takes place. Results were obtained from an experimental program carried out in a 3-MWe pilot plant. Additionally, five kinetic models, from the literature, of the reaction of sulfation of Ca(OH){sub 2} at low temperatures were assessed by simulation and indicate that the desulfurization efficiencies predicted by them are clearly lower than those experimentally obtained in our own pilot plant as well as others. Next, a general model was fitted by minimizing the difference between the calculated and the experimental results from the pilot plant, using Matlab{sup TM}. The parameters were reduced as much as possible, to only two. Finally, after implementing this model in a simulation tool of the in-duct sorbent injection process, it was validated and it was shown to yield a realistic approach useful for both analyzing results and aiding in the design of an in-duct desulfurization process.

Semantic modeling for theory clarification: The realist vs liberal international relations perspective

Energy Technology Data Exchange (ETDEWEB)

Bray, O.H. [Sandia National Labs., Albuquerque, NM (United States)]|[Univ. of New Mexico, Albuquerque, NM (United States). Political Science Dept.

1994-04-01

This paper describes a natural language based, semantic information modeling methodology and explores its use and value in clarifying and comparing political science theories and frameworks. As an example, the paper uses this methodology to clarify and compare some of the basic concepts and relationships in the realist (e.g. Waltz) and the liberal (e.g. Rosenau) paradigms for international relations. The methodology can provide three types of benefits: (1) it can clarify and make explicit exactly what is meant by a concept; (2) it can often identify unanticipated implications and consequence of concepts and relationships; and (3) it can help in identifying and operationalizing testable hypotheses.

Survey of Approaches to Generate Realistic Synthetic Graphs

Energy Technology Data Exchange (ETDEWEB)

Lim, Seung-Hwan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Sangkeun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Powers, Sarah S [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Imam, Neena [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-10-01

A graph is a flexible data structure that can represent relationships between entities. As with other data analysis tasks, the use of realistic graphs is critical to obtaining valid research results. Unfortunately, using the actual ("real-world") graphs for research and new algorithm development is difficult due to the presence of sensitive information in the data or due to the scale of data. This results in practitioners developing algorithms and systems that employ synthetic graphs instead of real-world graphs. Generating realistic synthetic graphs that provide reliable statistical confidence to algorithmic analysis and system evaluation involves addressing technical hurdles in a broad set of areas. This report surveys the state of the art in approaches to generate realistic graphs that are derived from fitted graph models on real-world graphs.

A realistic neural mass model of the cortex with laminar-specific connections and synaptic plasticity - evaluation with auditory habituation.

Directory of Open Access Journals (Sweden)

Peng Wang

Full Text Available In this work we propose a biologically realistic local cortical circuit model (LCCM, based on neural masses, that incorporates important aspects of the functional organization of the brain that have not been covered by previous models: (1 activity dependent plasticity of excitatory synaptic couplings via depleting and recycling of neurotransmitters and (2 realistic inter-laminar dynamics via laminar-specific distribution of and connections between neural populations. The potential of the LCCM was demonstrated by accounting for the process of auditory habituation. The model parameters were specified using Bayesian inference. It was found that: (1 besides the major serial excitatory information pathway (layer 4 to layer 2/3 to layer 5/6, there exists a parallel "short-cut" pathway (layer 4 to layer 5/6, (2 the excitatory signal flow from the pyramidal cells to the inhibitory interneurons seems to be more intra-laminar while, in contrast, the inhibitory signal flow from inhibitory interneurons to the pyramidal cells seems to be both intra- and inter-laminar, and (3 the habituation rates of the connections are unsymmetrical: forward connections (from layer 4 to layer 2/3 are more strongly habituated than backward connections (from Layer 5/6 to layer 4. Our evaluation demonstrates that the novel features of the LCCM are of crucial importance for mechanistic explanations of brain function. The incorporation of these features into a mass model makes them applicable to modeling based on macroscopic data (like EEG or MEG, which are usually available in human experiments. Our LCCM is therefore a valuable building block for future realistic models of human cognitive function.

Realistic Approach for Phasor Measurement Unit Placement

DEFF Research Database (Denmark)

Rather, Zakir Hussain; Chen, Zhe; Thøgersen, Paul

2015-01-01

This paper presents a realistic cost-effectivemodel for optimal placement of phasor measurement units (PMUs) for complete observability of a power system considering practical cost implications. The proposed model considers hidden or otherwise unaccounted practical costs involved in PMU...... installation. Consideration of these hidden but significant and integral part of total PMU installation costs was inspired from practical experience on a real-life project. The proposedmodel focuses on the minimization of total realistic costs instead of a widely used theoretical concept of a minimal number...... of PMUs. The proposed model has been applied to IEEE 14-bus, IEEE 24-bus, IEEE 30-bus, New England 39-bus, and large power system of 300 buses and real life Danish grid. A comparison of the presented results with those reported by traditionalmethods has also been shown to justify the effectiveness...

Mathematics Instructional Model Based on Realistic Mathematics Education to Promote Problem Solving Ability at Junior High School Padang

OpenAIRE

Edwin Musdi

2016-01-01

This research aims to develop a mathematics instructional model based realistic mathematics education (RME) to promote students' problem-solving abilities. The design research used Plomp models, which consists of preliminary phase, development or proto-typing phase and assessment phase.  At this study, only the first two phases conducted. The first phase, a preliminary investigation, carried out with a literature study to examine the theory-based instructional learning RME model, characterist...

Biochemical transport modeling, estimation, and detection in realistic environments

Science.gov (United States)

Ortner, Mathias; Nehorai, Arye

2006-05-01

Early detection and estimation of the spread of a biochemical contaminant are major issues for homeland security applications. We present an integrated approach combining the measurements given by an array of biochemical sensors with a physical model of the dispersion and statistical analysis to solve these problems and provide system performance measures. We approximate the dispersion model of the contaminant in a realistic environment through numerical simulations of reflected stochastic diffusions describing the microscopic transport phenomena due to wind and chemical diffusion using the Feynman-Kac formula. We consider arbitrary complex geometries and account for wind turbulence. Localizing the dispersive sources is useful for decontamination purposes and estimation of the cloud evolution. To solve the associated inverse problem, we propose a Bayesian framework based on a random field that is particularly powerful for localizing multiple sources with small amounts of measurements. We also develop a sequential detector using the numerical transport model we propose. Sequential detection allows on-line analysis and detecting wether a change has occurred. We first focus on the formulation of a suitable sequential detector that overcomes the presence of unknown parameters (e.g. release time, intensity and location). We compute a bound on the expected delay before false detection in order to decide the threshold of the test. For a fixed false-alarm rate, we obtain the detection probability of a substance release as a function of its location and initial concentration. Numerical examples are presented for two real-world scenarios: an urban area and an indoor ventilation duct.

Modeling shockwave deformation via molecular dynamics

International Nuclear Information System (INIS)

Holian, B.L.

1987-01-01

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

Open source molecular modeling.

Science.gov (United States)

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

2016-09-01

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

Implications of introducing realistic fire response traits in a Dynamic Global Vegetation Model

Science.gov (United States)

Kelley, D.; Harrison, S. P.; Prentice, I. C.

2013-12-01

Bark thickness is a key trait protecting woody plants against fire damage, while the ability to resprout is a trait that confers competitive advantage over non-resprouting individuals in fire-prone landscapes. Neither trait is well represented in fire-enabled dynamic global vegetation models (DGVMs). Here we describe a version of the Land Processes and eXchanges (LPX-Mv1) DGVM that incorporates both of these traits in a realistic way. From a synthesis of a large number of field studies, we show there is considerable innate variability in bark thickness between species within a plant-functional type (PFT). Furthermore, bark thickness is an adaptive trait at ecosystem level, increasing with fire frequency. We use the data to specify the range of bark thicknesses characteristic of each model PFT. We allow this distribution to change dynamically: thinner-barked trees are killed preferentially by fire, shifting the distribution of bark thicknesses represented in a model grid cell. We use the PFT-specific bark-thickness probability range for saplings during re-establishment. Since it is rare to destroy all trees in a grid cell, this treatment results in average bark thickness increasing with fire frequency and intensity. Resprouting is a prominent adaptation of temperate and tropical trees in fire-prone areas. The ability to resprout from above-ground tissue (apical or epicormic resprouting) results in the fastest recovery of total biomass after disturbance; resprouting from basal or below-ground meristems results in slower recovery, while non-resprouting species must regenerate from seed and therefore take the longest time to recover. Our analyses show that resprouting species have thicker bark than non-resprouting species. Investment in resprouting is accompanied by reduced efficacy of regeneration from seed. We introduce resprouting PFTs in LPX-Mv1 by specifying an appropriate range of bark thickness, allowing resprouters to survive fire and regenerate vegetatively in

An anatomically realistic whole-body pregnant-woman model and specific absorption rates for pregnant-woman exposure to electromagnetic plane waves from 10 MHz to 2 GHz

International Nuclear Information System (INIS)

Nagaoka, Tomoaki; Togashi, Toshihiro; Saito, Kazuyuki; Takahashi, Masaharu; Ito, Koichi; Watanabe, Soichi

2007-01-01

The numerical dosimetry of pregnant women is an important issue in electromagnetic-field safety. However, an anatomically realistic whole-body pregnant-woman model for electromagnetic dosimetry has not been developed. Therefore, we have developed a high-resolution whole-body model of pregnant women. A new fetus model including inherent tissues of pregnant women was constructed on the basis of abdominal magnetic resonance imaging data of a 26-week-pregnant woman. The whole-body pregnant-woman model was developed by combining the fetus model and a nonpregnant-woman model that was developed previously. The developed model consists of about 7 million cubical voxels of 2 mm size and is segmented into 56 tissues and organs. This pregnant-woman model is the first completely anatomically realistic voxel model that includes a realistic fetus model and enables a numerical simulation of electromagnetic dosimetry up to the gigahertz band. In this paper, we also present the basic specific absorption rate characteristics of the pregnant-woman model exposed to vertically and horizontally polarized electromagnetic waves from 10 MHz to 2 GHz

Realistic camera noise modeling with application to improved HDR synthesis

Science.gov (United States)

Goossens, Bart; Luong, Hiêp; Aelterman, Jan; Pižurica, Aleksandra; Philips, Wilfried

2012-12-01

Due to the ongoing miniaturization of digital camera sensors and the steady increase of the "number of megapixels", individual sensor elements of the camera become more sensitive to noise, even deteriorating the final image quality. To go around this problem, sophisticated processing algorithms in the devices, can help to maximally exploit the knowledge on the sensor characteristics (e.g., in terms of noise), and offer a better image reconstruction. Although a lot of research focuses on rather simplistic noise models, such as stationary additive white Gaussian noise, only limited attention has gone to more realistic digital camera noise models. In this article, we first present a digital camera noise model that takes several processing steps in the camera into account, such as sensor signal amplification, clipping, post-processing,.. We then apply this noise model to the reconstruction problem of high dynamic range (HDR) images from a small set of low dynamic range (LDR) exposures of a static scene. In literature, HDR reconstruction is mostly performed by computing a weighted average, in which the weights are directly related to the observer pixel intensities of the LDR image. In this work, we derive a Bayesian probabilistic formulation of a weighting function that is near-optimal in the MSE sense (or SNR sense) of the reconstructed HDR image, by assuming exponentially distributed irradiance values. We define the weighting function as the probability that the observed pixel intensity is approximately unbiased. The weighting function can be directly computed based on the noise model parameters, which gives rise to different symmetric and asymmetric shapes when electronic noise or photon noise is dominant. We also explain how to deal with the case that some of the noise model parameters are unknown and explain how the camera response function can be estimated using the presented noise model. Finally, experimental results are provided to support our findings.

Operator representation for effective realistic interactions

Energy Technology Data Exchange (ETDEWEB)

Weber, Dennis; Feldmeier, Hans; Neff, Thomas [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany)

2013-07-01

We present a method to derive an operator representation from the partial wave matrix elements of effective realistic nucleon-nucleon potentials. This method allows to employ modern effective interactions, which are mostly given in matrix element representation, also in nuclear many-body methods requiring explicitly the operator representation, for example ''Fermionic Molecular Dynamics'' (FMD). We present results for the operator representation of effective interactions obtained from the Argonne V18 potential with the Uenitary Correlation Operator Method'' (UCOM) and the ''Similarity Renormalization Group'' (SRG). Moreover, the operator representation allows a better insight in the nonlocal structure of the potential: While the UCOM transformed potential only shows a quadratic momentum dependence, the momentum dependence of SRG transformed potentials is beyond such a simple polynomial form.

Satisfaction and sustainability: a realist review of decentralized models of perinatal surgery for rural women.

Science.gov (United States)

Kornelsen, Jude; McCartney, Kevin; Williams, Kim

2016-01-01

This article was developed as part of a larger realist review investigating the viability and efficacy of decentralized models of perinatal surgical services for rural women in the context of recent and ongoing service centralization witnessed in many developed nations. The larger realist review was commissioned by the British Columbia Ministry of Health and Perinatal Services of British Columbia, Canada. Findings from that review are addressed in this article specific to the sustainability of rural perinatal surgical sites and the satisfaction of providers that underpins their recruitment to and retention at such sites. A realist method was used in the selection and analysis of literature with the intention to iteratively develop a sophisticated understanding of how perinatal surgical services can best meet the needs of women who live in rural and remote environments. The goal of a realist review is to examine what works for whom under what circumstances and why. The high sensitivity search used language (English) and year (since 1990) limiters in keeping with both a realist and rapid review tradition of using reasoned contextual boundaries. No exclusions were made based on methodology or methodological approach in keeping with a realist review. Databases searched included MEDLINE, PubMed, EBSCO, CINAHL, EBM Reviews, NHS Economic Evaluation Database and PAIS International for literature in December 2013. Database searching produced 103 included academic articles. A further 59 resources were added through pearling and 13 grey literature reports were added on recommendation from the commissioner. A total of 42 of these 175 articles were included in this article as specific to provider satisfaction and service sustainability. Operative perinatal practice was found to be a lynchpin of sustainable primary and surgical services in rural communities. Rural shortages of providers, including challenges with recruitment and retention, were found to be a complex issue, with

A Fibrocontractive Mechanochemical Model of Dermal Wound Closure Incorporating Realistic Growth Factor Kinetics

KAUST Repository

Murphy, Kelly E.

2012-01-13

Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.

A Fibrocontractive Mechanochemical Model of Dermal Wound Closure Incorporating Realistic Growth Factor Kinetics

KAUST Repository

Murphy, Kelly E.; Hall, Cameron L.; Maini, Philip K.; McCue, Scott W.; McElwain, D. L. Sean

2012-01-01

Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.

Improvement of Modeling Scheme of the Safety Injection Tank with Fluidic Device for Realistic LBLOCA Calculation

International Nuclear Information System (INIS)

Bang, Young Seok; Cheong, Aeju; Woo, Sweng Woong

2014-01-01

Confirmation of the performance of the SIT with FD should be based on thermal-hydraulic analysis of LBLOCA and an adequate and physical model simulating the SIT/FD should be used in the LBLOCA calculation. To develop such a physical model on SIT/FD, simulation of the major phenomena including flow distribution of by standpipe and FD should be justified by full scale experiment and/or plant preoperational testing. Author's previous study indicated that an approximation of SIT/FD phenomena could be obtained by a typical system transient code, MARS-KS, and using 'accumulator' component model, however, that additional improvement on modeling scheme of the FD and standpipe flow paths was needed for a reasonable prediction. One problem was a depressurizing behavior after switchover to low flow injection phase. Also a potential to release of nitrogen gas from the SIT to the downstream pipe and then reactor core through flow paths of FD and standpipe has been concerned. The intrusion of noncondensible gas may have an effect on LBLOCA thermal response. Therefore, a more reliable model on SIT/FD has been requested to get a more accurate prediction and a confidence of the evaluation of LBLOCA. The present paper is to discuss an improvement of modeling scheme from the previous study. Compared to the existing modeling, effect of the present modeling scheme on LBLOCA cladding thermal response is discussed. The present study discussed the modeling scheme of SIT with FD for a realistic simulation of LBLOCA of APR1400. Currently, the SIT blowdown test can be best simulated by the modeling scheme using 'pipe' component with dynamic area reduction. The LBLOCA analysis adopting the modeling scheme showed the PCT increase of 23K when compared to the case of 'accumulator' component model, which was due to the flow rate decrease at transition phase low flow injection and intrusion of nitrogen gas to the core. Accordingly, the effect of SIT/FD modeling

Measurable realistic image-based 3D mapping

Science.gov (United States)

Liu, W.; Wang, J.; Wang, J. J.; Ding, W.; Almagbile, A.

2011-12-01

Maps with 3D visual models are becoming a remarkable feature of 3D map services. High-resolution image data is obtained for the construction of 3D visualized models.The3D map not only provides the capabilities of 3D measurements and knowledge mining, but also provides the virtual experienceof places of interest, such as demonstrated in the Google Earth. Applications of 3D maps are expanding into the areas of architecture, property management, and urban environment monitoring. However, the reconstruction of high quality 3D models is time consuming, and requires robust hardware and powerful software to handle the enormous amount of data. This is especially for automatic implementation of 3D models and the representation of complicated surfacesthat still need improvements with in the visualisation techniques. The shortcoming of 3D model-based maps is the limitation of detailed coverage since a user can only view and measure objects that are already modelled in the virtual environment. This paper proposes and demonstrates a 3D map concept that is realistic and image-based, that enables geometric measurements and geo-location services. Additionally, image-based 3D maps provide more detailed information of the real world than 3D model-based maps. The image-based 3D maps use geo-referenced stereo images or panoramic images. The geometric relationships between objects in the images can be resolved from the geometric model of stereo images. The panoramic function makes 3D maps more interactive with users but also creates an interesting immersive circumstance. Actually, unmeasurable image-based 3D maps already exist, such as Google street view, but only provide virtual experiences in terms of photos. The topographic and terrain attributes, such as shapes and heights though are omitted. This paper also discusses the potential for using a low cost land Mobile Mapping System (MMS) to implement realistic image 3D mapping, and evaluates the positioning accuracy that a measureable

Realistic and efficient 2D crack simulation

Science.gov (United States)

Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

2010-04-01

Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

Using remotely sensed data and stochastic models to simulate realistic flood hazard footprints across the continental US

Science.gov (United States)

Bates, P. D.; Quinn, N.; Sampson, C. C.; Smith, A.; Wing, O.; Neal, J. C.

2017-12-01

Remotely sensed data has transformed the field of large scale hydraulic modelling. New digital elevation, hydrography and river width data has allowed such models to be created for the first time, and remotely sensed observations of water height, slope and water extent has allowed them to be calibrated and tested. As a result, we are now able to conduct flood risk analyses at national, continental or even global scales. However, continental scale analyses have significant additional complexity compared to typical flood risk modelling approaches. Traditional flood risk assessment uses frequency curves to define the magnitude of extreme flows at gauging stations. The flow values for given design events, such as the 1 in 100 year return period flow, are then used to drive hydraulic models in order to produce maps of flood hazard. Such an approach works well for single gauge locations and local models because over relatively short river reaches (say 10-60km) one can assume that the return period of an event does not vary. At regional to national scales and across multiple river catchments this assumption breaks down, and for a given flood event the return period will be different at different gauging stations, a pattern known as the event `footprint'. Despite this, many national scale risk analyses still use `constant in space' return period hazard layers (e.g. the FEMA Special Flood Hazard Areas) in their calculations. Such an approach can estimate potential exposure, but will over-estimate risk and cannot determine likely flood losses over a whole region or country. We address this problem by using a stochastic model to simulate many realistic extreme event footprints based on observed gauged flows and the statistics of gauge to gauge correlations. We take the entire USGS gauge data catalogue for sites with > 45 years of record and use a conditional approach for multivariate extreme values to generate sets of flood events with realistic return period variation in

Realistic modeling of seismic input for megacities and large urban areas

Science.gov (United States)

Panza, G. F.; Unesco/Iugs/Igcp Project 414 Team

2003-04-01

The project addressed the problem of pre-disaster orientation: hazard prediction, risk assessment, and hazard mapping, in connection with seismic activity and man-induced vibrations. The definition of realistic seismic input has been obtained from the computation of a wide set of time histories and spectral information, corresponding to possible seismotectonic scenarios for different source and structural models. The innovative modeling technique, that constitutes the common tool to the entire project, takes into account source, propagation and local site effects. This is done using first principles of physics about wave generation and propagation in complex media, and does not require to resort to convolutive approaches, that have been proven to be quite unreliable, mainly when dealing with complex geological structures, the most interesting from the practical point of view. In fact, several techniques that have been proposed to empirically estimate the site effects using observations convolved with theoretically computed signals corresponding to simplified models, supply reliable information about the site response to non-interfering seismic phases. They are not adequate in most of the real cases, when the seismic sequel is formed by several interfering waves. The availability of realistic numerical simulations enables us to reliably estimate the amplification effects even in complex geological structures, exploiting the available geotechnical, lithological, geophysical parameters, topography of the medium, tectonic, historical, palaeoseismological data, and seismotectonic models. The realistic modeling of the ground motion is a very important base of knowledge for the preparation of groundshaking scenarios that represent a valid and economic tool for the seismic microzonation. This knowledge can be very fruitfully used by civil engineers in the design of new seismo-resistant constructions and in the reinforcement of the existing built environment, and, therefore

Structural Origins of Conductance Fluctuations in Gold–Thiolate Molecular Transport Junctions

KAUST Repository

French, William R.

2013-03-21

We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (where the electrodes are modeled as flat surfaces) to structurally realistic, experimentally representative junctions resulting from break-junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with nondeformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance, and also to theoreticians invoking simplified structural models of junctions to predict their behavior. © 2013 American Chemical Society.

Structural Origins of Conductance Fluctuations in Gold–Thiolate Molecular Transport Junctions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-01-01

We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (where the electrodes are modeled as flat surfaces) to structurally realistic, experimentally representative junctions resulting from break-junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with nondeformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance, and also to theoreticians invoking simplified structural models of junctions to predict their behavior. © 2013 American Chemical Society.

Effective electric fields along realistic DTI-based neural trajectories for modelling the stimulation mechanisms of TMS

International Nuclear Information System (INIS)

De Geeter, N; Crevecoeur, G; Dupré, L; Leemans, A

2015-01-01

In transcranial magnetic stimulation (TMS), an applied alternating magnetic field induces an electric field in the brain that can interact with the neural system. It is generally assumed that this induced electric field is the crucial effect exciting a certain region of the brain. More specifically, it is the component of this field parallel to the neuron’s local orientation, the so-called effective electric field, that can initiate neuronal stimulation. Deeper insights on the stimulation mechanisms can be acquired through extensive TMS modelling. Most models study simple representations of neurons with assumed geometries, whereas we embed realistic neural trajectories computed using tractography based on diffusion tensor images. This way of modelling ensures a more accurate spatial distribution of the effective electric field that is in addition patient and case specific. The case study of this paper focuses on the single pulse stimulation of the left primary motor cortex with a standard figure-of-eight coil. Including realistic neural geometry in the model demonstrates the strong and localized variations of the effective electric field between the tracts themselves and along them due to the interplay of factors such as the tract’s position and orientation in relation to the TMS coil, the neural trajectory and its course along the white and grey matter interface. Furthermore, the influence of changes in the coil orientation is studied. Investigating the impact of tissue anisotropy confirms that its contribution is not negligible. Moreover, assuming isotropic tissues lead to errors of the same size as rotating or tilting the coil with 10 degrees. In contrast, the model proves to be less sensitive towards the not well-known tissue conductivity values. (paper)

Smart-DS: Synthetic Models for Advanced, Realistic Testing: Distribution Systems and Scenarios

Energy Technology Data Exchange (ETDEWEB)

Krishnan, Venkat K [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Palmintier, Bryan S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hodge, Brian S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hale, Elaine T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Elgindy, Tarek [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bugbee, Bruce [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Rossol, Michael N [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Lopez, Anthony J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Krishnamurthy, Dheepak [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Vergara, Claudio [MIT; Domingo, Carlos Mateo [IIT Comillas; Postigo, Fernando [IIT Comillas; de Cuadra, Fernando [IIT Comillas; Gomez, Tomas [IIT Comillas; Duenas, Pablo [MIT; Luke, Max [MIT; Li, Vivian [MIT; Vinoth, Mohan [GE Grid Solutions; Kadankodu, Sree [GE Grid Solutions

2017-08-09

The National Renewable Energy Laboratory (NREL) in collaboration with Massachusetts Institute of Technology (MIT), Universidad Pontificia Comillas (Comillas-IIT, Spain) and GE Grid Solutions, is working on an ARPA-E GRID DATA project, titled Smart-DS, to create: 1) High-quality, realistic, synthetic distribution network models, and 2) Advanced tools for automated scenario generation based on high-resolution weather data and generation growth projections. Through these advancements, the Smart-DS project is envisioned to accelerate the development, testing, and adoption of advanced algorithms, approaches, and technologies for sustainable and resilient electric power systems, especially in the realm of U.S. distribution systems. This talk will present the goals and overall approach of the Smart-DS project, including the process of creating the synthetic distribution datasets using reference network model (RNM) and the comprehensive validation process to ensure network realism, feasibility, and applicability to advanced use cases. The talk will provide demonstrations of early versions of synthetic models, along with the lessons learnt from expert engagements to enhance future iterations. Finally, the scenario generation framework, its development plans, and co-ordination with GRID DATA repository teams to house these datasets for public access will also be discussed.

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,…

Quantifying and Visualizing Uncertainties in Molecular Models

OpenAIRE

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

2015-01-01

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

On the impacts of coarse-scale models of realistic roughness on a forward-facing step turbulent flow

International Nuclear Information System (INIS)

Wu, Yanhua; Ren, Huiying

2013-01-01

Highlights: ► Discrete wavelet transform was used to produce coarse-scale models of roughness. ► PIV were performed in a forward-facing step flow with roughness of different scales. ► Impacts of roughness scales on various turbulence statistics were studied. -- Abstract: The present work explores the impacts of the coarse-scale models of realistic roughness on the turbulent boundary layers over forward-facing steps. The surface topographies of different scale resolutions were obtained from a novel multi-resolution analysis using discrete wavelet transform. PIV measurements are performed in the streamwise–wall-normal (x–y) planes at two different spanwise positions in turbulent boundary layers at Re h = 3450 and δ/h = 8, where h is the mean step height and δ is the incoming boundary layer thickness. It was observed that large-scale but low-amplitude roughness scales had small effects on the forward-facing step turbulent flow. For the higher-resolution model of the roughness, the turbulence characteristics within 2h downstream of the steps are observed to be distinct from those over the original realistic rough step at a measurement position where the roughness profile possesses a positive slope immediately after the step’s front. On the other hand, much smaller differences exist in the flow characteristics at the other measurement position whose roughness profile possesses a negative slope following the step’s front

Nonlinear dynamics of zigzag molecular chains (in Russian)

DEFF Research Database (Denmark)

Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

1999-01-01

models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...

QSAR models based on quantum topological molecular similarity.

Science.gov (United States)

Popelier, P L A; Smith, P J

2006-07-01

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

Deep Generative Models for Molecular Science

DEFF Research Database (Denmark)

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

2018-01-01

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

Simulating the value of electric-vehicle-grid integration using a behaviourally realistic model

Science.gov (United States)

Wolinetz, Michael; Axsen, Jonn; Peters, Jotham; Crawford, Curran

2018-02-01

Vehicle-grid integration (VGI) uses the interaction between electric vehicles and the electrical grid to provide benefits that may include reducing the cost of using intermittent renwable electricity or providing a financial incentive for electric vehicle ownerhip. However, studies that estimate the value of VGI benefits have largely ignored how consumer behaviour will affect the magnitude of the impact. Here, we simulate the long-term impact of VGI using behaviourally realistic and empirically derived models of vehicle adoption and charging combined with an electricity system model. We focus on the case where a central entity manages the charging rate and timing for participating electric vehicles. VGI is found not to increase the adoption of electric vehicles, but does have a a small beneficial impact on electricity prices. By 2050, VGI reduces wholesale electricity prices by 0.6-0.7% (0.7 MWh-1, 2010 CAD) relative to an equivalent scenario without VGI. Excluding consumer behaviour from the analysis inflates the value of VGI.

The ultimate intrinsic signal-to-noise ratio of loop- and dipole-like current patterns in a realistic human head model.

Science.gov (United States)

Pfrommer, Andreas; Henning, Anke

2018-03-13

The ultimate intrinsic signal-to-noise ratio (UISNR) represents an upper bound for the achievable SNR of any receive coil. To reach this threshold a complete basis set of equivalent surface currents is required. This study systematically investigated to what extent either loop- or dipole-like current patterns are able to reach the UISNR threshold in a realistic human head model between 1.5 T and 11.7 T. Based on this analysis, we derived guidelines for coil designers to choose the best array element at a given field strength. Moreover, we present ideal current patterns yielding the UISNR in a realistic body model. We distributed generic current patterns on a cylindrical and helmet-shaped surface around a realistic human head model. We excited electromagnetic fields in the human head by using eigenfunctions of the spherical and cylindrical Helmholtz operator. The electromagnetic field problem was solved by a fast volume integral equation solver. At 7 T and above, adding curl-free current patterns to divergence-free current patterns substantially increased the SNR in the human head (locally >20%). This was true for the helmet-shaped and the cylindrical surface. On the cylindrical surface, dipole-like current patterns had high SNR performance in central regions at ultra-high field strength. The UISNR increased superlinearly with B0 in most parts of the cerebrum but only sublinearly in the periphery of the human head. The combination of loop and dipole elements could enhance the SNR performance in the human head at ultra-high field strength. © 2018 International Society for Magnetic Resonance in Medicine.

Details of regional particle deposition and airflow structures in a realistic model of human tracheobronchial airways: two-phase flow simulation.

Science.gov (United States)

Rahimi-Gorji, Mohammad; Gorji, Tahereh B; Gorji-Bandpy, Mofid

2016-07-01

In the present investigation, detailed two-phase flow modeling of airflow, transport and deposition of micro-particles (1-10µm) in a realistic tracheobronchial airway geometry based on CT scan images under various breathing conditions (i.e. 10-60l/min) was considered. Lagrangian particle tracking has been used to investigate the particle deposition patterns in a model comprising mouth up to generation G6 of tracheobronchial airways. The results demonstrated that during all breathing patterns, the maximum velocity change occurred in the narrow throat region (Larynx). Due to implementing a realistic geometry for simulations, many irregularities and bending deflections exist in the airways model. Thereby, at higher inhalation rates, these areas are prone to vortical effects which tend to entrap the inhaled particles. According to the results, deposition fraction has a direct relationship with particle aerodynamic diameter (for dp=1-10µm). Enhancing inhalation flow rate and particle size will largely increase the inertial force and consequently, more particle deposition is evident suggesting that inertial impaction is the dominant deposition mechanism in tracheobronchial airways. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spectroscopy of light nuclei with realistic NN interaction JISP

International Nuclear Information System (INIS)

Shirokov, A. M.; Vary, J. P.; Mazur, A. I.; Weber, T. A.

2008-01-01

Recent results of our systematic ab initio studies of the spectroscopy of s- and p-shell nuclei in fully microscopic large-scale (up to a few hundred million basis functions) no-core shell-model calculations are presented. A new high-quality realistic nonlocal NN interaction JISP is used. This interaction is obtained in the J-matrix inverse-scattering approach (JISP stands for the J-matrix inverse-scattering potential) and is of the form of a small-rank matrix in the oscillator basis in each of the NN partial waves, providing a very fast convergence in shell-model studies. The current purely two-body JISP model of the nucleon-nucleon interaction JISP16 provides not only an excellent description of two-nucleon data (deuteron properties and np scattering) with χ 2 /datum = 1.05 but also a better description of a wide range of observables (binding energies, spectra, rms radii, quadrupole moments, electromagnetic-transition probabilities, etc.) in all s-and p-shell nuclei than the best modern interaction models combining realistic nucleon-nucleon and three-nucleon interactions.

Larval dispersal modeling of pearl oyster Pinctada margaritifera following realistic environmental and biological forcing in Ahe atoll lagoon.

Directory of Open Access Journals (Sweden)

Yoann Thomas

Full Text Available Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera is cultured extensively to produce black pearls, especially in French Polynesia's atoll lagoons. This aquaculture relies on spat collection, a process that can be optimized by understanding which factors influence larval dispersal. Here, we investigate the sensitivity of P. margaritifera larval dispersal kernel to both physical and biological factors in the lagoon of Ahe atoll. Specifically, using a validated 3D larval dispersal model, the variability of lagoon-scale connectivity is investigated against wind forcing, depth and location of larval release, destination location, vertical swimming behavior and pelagic larval duration (PLD factors. The potential connectivity was spatially weighted according to both the natural and cultivated broodstock densities to provide a realistic view of connectivity. We found that the mean pattern of potential connectivity was driven by the southwest and northeast main barotropic circulation structures, with high retention levels in both. Destination locations, spawning sites and PLD were the main drivers of potential connectivity, explaining respectively 26%, 59% and 5% of the variance. Differences between potential and realistic connectivity showed the significant contribution of the pearl oyster broodstock location to its own dynamics. Realistic connectivity showed larger larval supply in the western destination locations, which are preferentially used by farmers for spat collection. In addition, larval supply in the same sectors was enhanced during summer wind conditions. These results provide new cues to understanding the dynamics of bottom-dwelling populations in atoll lagoons, and show how to take advantage of numerical models for pearl oyster management.

Laserlike Vibrational Instability in Rectifying Molecular Conductors

DEFF Research Database (Denmark)

Lu, Jing Tao; Hedegård, Per; Brandbyge, Mads

2011-01-01

We study the damping of molecular vibrations due to electron-hole pair excitations in donor-acceptor (D-A) type molecular rectifiers. At finite voltage additional nonequilibrium electron-hole pair excitations involving both electrodes become possible, and contribute to the stimulated emission....... We investigate the effect in realistic molecular rectifier structures using first-principles calculations....

Realistic roofs over a rectilinear polygon

KAUST Repository

Ahn, Heekap

2013-11-01

Given a simple rectilinear polygon P in the xy-plane, a roof over P is a terrain over P whose faces are supported by planes through edges of P that make a dihedral angle π/4 with the xy-plane. According to this definition, some roofs may have faces isolated from the boundary of P or even local minima, which are undesirable for several practical reasons. In this paper, we introduce realistic roofs by imposing a few additional constraints. We investigate the geometric and combinatorial properties of realistic roofs and show that the straight skeleton induces a realistic roof with maximum height and volume. We also show that the maximum possible number of distinct realistic roofs over P is ((n-4)(n-4)/4 /2⌋) when P has n vertices. We present an algorithm that enumerates a combinatorial representation of each such roof in O(1) time per roof without repetition, after O(n4) preprocessing time. We also present an O(n5)-time algorithm for computing a realistic roof with minimum height or volume. © 2013 Elsevier B.V.

PIV-measured versus CFD-predicted flow dynamics in anatomically realistic cerebral aneurysm models.

Science.gov (United States)

Ford, Matthew D; Nikolov, Hristo N; Milner, Jaques S; Lownie, Stephen P; Demont, Edwin M; Kalata, Wojciech; Loth, Francis; Holdsworth, David W; Steinman, David A

2008-04-01

Computational fluid dynamics (CFD) modeling of nominally patient-specific cerebral aneurysms is increasingly being used as a research tool to further understand the development, prognosis, and treatment of brain aneurysms. We have previously developed virtual angiography to indirectly validate CFD-predicted gross flow dynamics against the routinely acquired digital subtraction angiograms. Toward a more direct validation, here we compare detailed, CFD-predicted velocity fields against those measured using particle imaging velocimetry (PIV). Two anatomically realistic flow-through phantoms, one a giant internal carotid artery (ICA) aneurysm and the other a basilar artery (BA) tip aneurysm, were constructed of a clear silicone elastomer. The phantoms were placed within a computer-controlled flow loop, programed with representative flow rate waveforms. PIV images were collected on several anterior-posterior (AP) and lateral (LAT) planes. CFD simulations were then carried out using a well-validated, in-house solver, based on micro-CT reconstructions of the geometries of the flow-through phantoms and inlet/outlet boundary conditions derived from flow rates measured during the PIV experiments. PIV and CFD results from the central AP plane of the ICA aneurysm showed a large stable vortex throughout the cardiac cycle. Complex vortex dynamics, captured by PIV and CFD, persisted throughout the cardiac cycle on the central LAT plane. Velocity vector fields showed good overall agreement. For the BA, aneurysm agreement was more compelling, with both PIV and CFD similarly resolving the dynamics of counter-rotating vortices on both AP and LAT planes. Despite the imposition of periodic flow boundary conditions for the CFD simulations, cycle-to-cycle fluctuations were evident in the BA aneurysm simulations, which agreed well, in terms of both amplitudes and spatial distributions, with cycle-to-cycle fluctuations measured by PIV in the same geometry. The overall good agreement

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.

Science.gov (United States)

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik; Harvey, Jeremy N; Mulholland, Adrian J

2016-06-20

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, but this is not a prerequisite for reaction via either mechanism. Several active site residues play a role in the binding of mexiletine in the active site, including Thr124 and Phe226. This work reveals key details of the N-hydroxylation of mexiletine and further demonstrates that mechanistic studies using QM/MM methods are useful for understanding drug metabolism.

Rapidly re-computable EEG (electroencephalography) forward models for realistic head shapes

International Nuclear Information System (INIS)

Ermer, J.J.; Mosher, J.C.; Baillet, S.; Leahy, R.M.

2001-01-01

Solution of the EEG source localization (inverse) problem utilizing model-based methods typically requires a significant number of forward model evaluations. For subspace based inverse methods like MUSIC (6), the total number of forward model evaluations can often approach an order of 10 3 or 10 4 . Techniques based on least-squares minimization may require significantly more evaluations. The observed set of measurements over an M-sensor array is often expressed as a linear forward spatio-temporal model of the form: F = GQ + N (1) where the observed forward field F (M-sensors x N-time samples) can be expressed in terms of the forward model G, a set of dipole moment(s) Q (3xP-dipoles x N-time samples) and additive noise N. Because of their simplicity, ease of computation, and relatively good accuracy, multi-layer spherical models (7) (or fast approximations described in (1), (7)) have traditionally been the 'forward model of choice' for approximating the human head. However, approximation of the human head via a spherical model does have several key drawbacks. By its very shape, the use of a spherical model distorts the true distribution of passive currents in the skull cavity. Spherical models also require that the sensor positions be projected onto the fitted sphere (Fig. 1), resulting in a distortion of the true sensor-dipole spatial geometry (and ultimately the computed surface potential). The use of a single 'best-fitted' sphere has the added drawback of incomplete coverage of the inner skull region, often ignoring areas such as the frontal cortex. In practice, this problem is typically countered by fitting additional sphere(s) to those region(s) not covered by the primary sphere. The use of these additional spheres results in added complication to the forward model. Using high-resolution spatial information obtained via X-ray CT or MR imaging, a realistic head model can be formed by tessellating the head into a set of contiguous regions (typically the scalp

Modeling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-01-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri-coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminum atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author) [fr

Modelling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

Ganster, P.

2004-10-01

A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

Calculation of electrical potentials on the surface of a realistic head model by finite differences

International Nuclear Information System (INIS)

Lemieux, L.; McBride, A.; Hand, J.W.

1996-01-01

We present a method for the calculation of electrical potentials at the surface of realistic head models from a point dipole generator based on a 3D finite-difference algorithm. The model was validated by comparing calculated values with those obtained algebraically for a three-shell spherical model. For a 1.25 mm cubic grid size, the mean error was 4.9% for a superficial dipole (3.75 mm from the inner surface of the skull) pointing in the radial direction. The effect of generator discretization and node spacing on the accuracy of the model was studied. Three values of the node spacing were considered: 1, 1.25 and 1.5 mm. The mean relative errors were 4.2, 6.3 and 9.3%, respectively. The quality of the approximation of a point dipole by an array of nodes in a spherical neighbourhood did not depend significantly on the number of nodes used. The application of the method to a conduction model derived from MRI data is demonstrated. (author)

Realistic modelling of observed seismic motion in complex sedimentary basins

International Nuclear Information System (INIS)

Faeh, D.; Panza, G.F.

1994-03-01

Three applications of a numerical technique are illustrated to model realistically the seismic ground motion for complex two-dimensional structures. First we consider a sedimentary basin in the Friuli region, and we model strong motion records from an aftershock of the 1976 earthquake. Then we simulate the ground motion caused in Rome by the 1915, Fucino (Italy) earthquake, and we compare our modelling with the damage distribution observed in the town. Finally we deal with the interpretation of ground motion recorded in Mexico City, as a consequence of earthquakes in the Mexican subduction zone. The synthetic signals explain the major characteristics (relative amplitudes, spectral amplification, frequency content) of the considered seismograms, and the space distribution of the available macroseismic data. For the sedimentary basin in the Friuli area, parametric studies demonstrate the relevant sensitivity of the computed ground motion to small changes in the subsurface topography of the sedimentary basin, and in the velocity and quality factor of the sediments. The total energy of ground motion, determined from our numerical simulation in Rome, is in very good agreement with the distribution of damage observed during the Fucino earthquake. For epicentral distances in the range 50km-100km, the source location and not only the local soil conditions control the local effects. For Mexico City, the observed ground motion can be explained as resonance effects and as excitation of local surface waves, and the theoretical and the observed maximum spectral amplifications are very similar. In general, our numerical simulations permit the estimate of the maximum and average spectral amplification for specific sites, i.e. are a very powerful tool for accurate micro-zonation. (author). 38 refs, 19 figs, 1 tab

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

Directory of Open Access Journals (Sweden)

Rong Shen

2015-10-01

Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

The cognitive life of mechanical molecular models.

Science.gov (United States)

Charbonneau, Mathieu

2013-12-01

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

A Realistic Human Exposure Assessment of Indoor Radon released from Groundwater

International Nuclear Information System (INIS)

Yu, Dong Han; Han, Moon Hee

2002-01-01

The work presents a realistic human exposure assessment of indoor radon released from groundwater in a house. At first, a two-compartment model is developed to describe the generation and transfer of radon in indoor air from groundwater. The model is used to estimate radon concentrations profile of indoor air in a house using by showering, washing clothes, and flushing toilets. Then, the study performs an uncertainty analysis of model input parameters to quantify the uncertainty in radon concentration profile. In order to estimate a daily internal dose of a specific tissue group in an adult through the inhalation of such indoor radon, a PBPK(Physiologically-Based Pharmaco-Kinetic) model is developed. Combining indoor radon profile and PBPK model is used to a realistic human assessment for such exposure. The results obtained from this study would be used to the evaluation of human risk by inhalation associated with the indoor radon released from groundwater

Flow visualization through particle image velocimetry in realistic model of rhesus monkey's upper airway.

Science.gov (United States)

Kim, Ji-Woong; Phuong, Nguyen Lu; Aramaki, Shin-Ichiro; Ito, Kazuhide

2018-05-01

Studies concerning inhalation toxicology and respiratory drug-delivery systems require biological testing involving experiments performed on animals. Particle image velocimetry (PIV) is an effective in vitro technique that reveals detailed inhalation flow patterns, thereby assisting analyses of inhalation exposure to various substances. A realistic model of a rhesus-monkey upper airway was developed to investigate flow patterns in its oral and nasal cavities through PIV experiments performed under steady-state constant inhalation conditions at various flow rates-4, 10, and 20 L/min. Flow rate of the fluid passing through the inlet into the trachea was measured to obtain characteristic flow mechanisms, and flow phenomena in the model were confirmed via characterized flow fields. It was observed that increase in flow rate leads to constant velocity profiles in upper and lower trachea regions. It is expected that the results of this study would contribute to future validation of studies aimed at developing in silico models, especially those involving computational fluid dynamic (CFD) analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Experimental Section: On the magnetic field distribution generated by a dipolar current source situated in a realistically shaped compartment model of the head

NARCIS (Netherlands)

Meijs, J.W.H.; Bosch, F.G.C.; Peters, M.J.; Lopes da silva, F.H.

1987-01-01

The magnetic field distribution around the head is simulated using a realistically shaped compartment model of the head. The model is based on magnetic resonance images. The 3 compartments describe the brain, the skull and the scalp. The source is represented by a current dipole situated in the

Design and validation of realistic breast models for use in multiple alternative forced choice virtual clinical trials.

Science.gov (United States)

Elangovan, Premkumar; Mackenzie, Alistair; Dance, David R; Young, Kenneth C; Cooke, Victoria; Wilkinson, Louise; Given-Wilson, Rosalind M; Wallis, Matthew G; Wells, Kevin

2017-04-07

A novel method has been developed for generating quasi-realistic voxel phantoms which simulate the compressed breast in mammography and digital breast tomosynthesis (DBT). The models are suitable for use in virtual clinical trials requiring realistic anatomy which use the multiple alternative forced choice (AFC) paradigm and patches from the complete breast image. The breast models are produced by extracting features of breast tissue components from DBT clinical images including skin, adipose and fibro-glandular tissue, blood vessels and Cooper's ligaments. A range of different breast models can then be generated by combining these components. Visual realism was validated using a receiver operating characteristic (ROC) study of patches from simulated images calculated using the breast models and from real patient images. Quantitative analysis was undertaken using fractal dimension and power spectrum analysis. The average areas under the ROC curves for 2D and DBT images were 0.51  ±  0.06 and 0.54  ±  0.09 demonstrating that simulated and real images were statistically indistinguishable by expert breast readers (7 observers); errors represented as one standard error of the mean. The average fractal dimensions (2D, DBT) for real and simulated images were (2.72  ±  0.01, 2.75  ±  0.01) and (2.77  ±  0.03, 2.82  ±  0.04) respectively; errors represented as one standard error of the mean. Excellent agreement was found between power spectrum curves of real and simulated images, with average β values (2D, DBT) of (3.10  ±  0.17, 3.21  ±  0.11) and (3.01  ±  0.32, 3.19  ±  0.07) respectively; errors represented as one standard error of the mean. These results demonstrate that radiological images of these breast models realistically represent the complexity of real breast structures and can be used to simulate patches from mammograms and DBT images that are indistinguishable from

Electromagnetic forward modelling for realistic Earth models using unstructured tetrahedral meshes and a meshfree approach

Science.gov (United States)

Farquharson, C.; Long, J.; Lu, X.; Lelievre, P. G.

2017-12-01

makes the process of building a geophysical Earth model from a geological model much simpler. In this presentation we will explore the issues that arise when working with realistic Earth models and when synthesizing geophysical electromagnetic data for them. We briefly consider meshfree methods as a possible means of alleviating some of these issues.

Dynamical symmetries of molecular states in atomic, nuclear and hadron physics

International Nuclear Information System (INIS)

Iachello, F.; Cseh, J.; Levai, G.

1995-01-01

The algebraic description of dipole degrees of freedom is discussed. These degrees of freedom are relevant to two and few-body systems, as well as in the collective motion of many-body systems. Applications to molecular, nuclear and hadron spectroscopy are presented. Different internal degrees of freedom can also be coupled to the spatial ones, leading to realistic models of several complex systems. (author)

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.

Blend Shape Interpolation and FACS for Realistic Avatar

Science.gov (United States)

Alkawaz, Mohammed Hazim; Mohamad, Dzulkifli; Basori, Ahmad Hoirul; Saba, Tanzila

2015-03-01

The quest of developing realistic facial animation is ever-growing. The emergence of sophisticated algorithms, new graphical user interfaces, laser scans and advanced 3D tools imparted further impetus towards the rapid advancement of complex virtual human facial model. Face-to-face communication being the most natural way of human interaction, the facial animation systems became more attractive in the information technology era for sundry applications. The production of computer-animated movies using synthetic actors are still challenging issues. Proposed facial expression carries the signature of happiness, sadness, angry or cheerful, etc. The mood of a particular person in the midst of a large group can immediately be identified via very subtle changes in facial expressions. Facial expressions being very complex as well as important nonverbal communication channel are tricky to synthesize realistically using computer graphics. Computer synthesis of practical facial expressions must deal with the geometric representation of the human face and the control of the facial animation. We developed a new approach by integrating blend shape interpolation (BSI) and facial action coding system (FACS) to create a realistic and expressive computer facial animation design. The BSI is used to generate the natural face while the FACS is employed to reflect the exact facial muscle movements for four basic natural emotional expressions such as angry, happy, sad and fear with high fidelity. The results in perceiving the realistic facial expression for virtual human emotions based on facial skin color and texture may contribute towards the development of virtual reality and game environment of computer aided graphics animation systems.

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

Science.gov (United States)

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

2016-11-28

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

Development of Realistic Head Models for Electromagnetic Source Imaging of the Human Brain

National Research Council Canada - National Science Library

Akalin, Z

2001-01-01

... images is performed Then triangular, quadratic meshes are formed for the interfaces of the tissues, Thus, realistic meshes, representing scalp, skull, CSF, brain and eye tissues, are formed, At least...

Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

Energy Technology Data Exchange (ETDEWEB)

Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J. [Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Campus Cantoblanco, 28049 Madrid (Spain); Beljonne, D. [Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000 Mons (Belgium)

2015-09-21

Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

International Management: Creating a More Realistic Global Planning Environment.

Science.gov (United States)

Waldron, Darryl G.

2000-01-01

Discusses the need for realistic global planning environments in international business education, introducing a strategic planning model that has teams interacting with teams to strategically analyze a selected multinational company. This dynamic process must result in a single integrated written analysis that specifies an optimal strategy for…

Development and application of a deterministic-realistic hybrid methodology for LOCA licensing analysis

International Nuclear Information System (INIS)

Liang, Thomas K.S.; Chou, Ling-Yao; Zhang, Zhongwei; Hsueh, Hsiang-Yu; Lee, Min

2011-01-01

Highlights: → A new LOCA licensing methodology (DRHM, deterministic-realistic hybrid methodology) was developed. → DRHM involves conservative Appendix K physical models and statistical treatment of plant status uncertainties. → DRHM can generate 50-100 K PCT margin as compared to a traditional Appendix K methodology. - Abstract: It is well recognized that a realistic LOCA analysis with uncertainty quantification can generate greater safety margin as compared with classical conservative LOCA analysis using Appendix K evaluation models. The associated margin can be more than 200 K. To quantify uncertainty in BELOCA analysis, generally there are two kinds of uncertainties required to be identified and quantified, which involve model uncertainties and plant status uncertainties. Particularly, it will take huge effort to systematically quantify individual model uncertainty of a best estimate LOCA code, such as RELAP5 and TRAC. Instead of applying a full ranged BELOCA methodology to cover both model and plant status uncertainties, a deterministic-realistic hybrid methodology (DRHM) was developed to support LOCA licensing analysis. Regarding the DRHM methodology, Appendix K deterministic evaluation models are adopted to ensure model conservatism, while CSAU methodology is applied to quantify the effect of plant status uncertainty on PCT calculation. Generally, DRHM methodology can generate about 80-100 K margin on PCT as compared to Appendix K bounding state LOCA analysis.

Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

CERN Document Server

Farantos, Stavros C

2014-01-01

This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

Successful N2 leptogenesis with flavour coupling effects in realistic unified models

International Nuclear Information System (INIS)

Bari, Pasquale Di; King, Stephen F.

2015-01-01

In realistic unified models involving so-called SO(10)-inspired patterns of Dirac and heavy right-handed (RH) neutrino masses, the lightest right-handed neutrino N 1 is too light to yield successful thermal leptogenesis, barring highly fine tuned solutions, while the second heaviest right-handed neutrino N 2 is typically in the correct mass range. We show that flavour coupling effects in the Boltzmann equations may be crucial to the success of such N 2 dominated leptogenesis, by helping to ensure that the flavour asymmetries produced at the N 2 scale survive N 1 washout. To illustrate these effects we focus on N 2 dominated leptogenesis in an existing model, the A to Z of flavour with Pati-Salam, where the neutrino Dirac mass matrix may be equal to an up-type quark mass matrix and has a particular constrained structure. The numerical results, supported by analytical insight, show that in order to achieve successful N 2 leptogenesis, consistent with neutrino phenomenology, requires a ''flavour swap scenario'' together with a less hierarchical pattern of RH neutrino masses than naively expected, at the expense of some mild fine-tuning. In the considered A to Z model neutrino masses are predicted to be normal ordered, with an atmospheric neutrino mixing angle well into the second octant and the Dirac phase δ≅ 20 o , a set of predictions that will be tested in the next years in neutrino oscillation experiments. Flavour coupling effects may be relevant for other SO(10)-inspired unified models where N 2 leptogenesis is necessary

Toward realistic pursuit-evasion using a roadmap-based approach

KAUST Repository

Rodriguez, Samuel

2011-05-01

In this work, we describe an approach for modeling and simulating group behaviors for pursuit-evasion that uses a graph-based representation of the environment and integrates multi-agent simulation with roadmap-based path planning. Our approach can be applied to more realistic scenarios than are typically studied in most previous work, including agents moving in 3D environments such as terrains, multi-story buildings, and dynamic environments. We also support more realistic three-dimensional visibility computations that allow evading agents to hide in crowds or behind hills. We demonstrate the utility of this approach on mobile robots and in simulation for a variety of scenarios including pursuit-evasion and tag on terrains, in multi-level buildings, and in crowds. © 2011 IEEE.

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 ...

Molecular Modeling of Aerospace Polymer Matrices Including Carbon Nanotube-Enhanced Epoxy

Science.gov (United States)

Radue, Matthew S.

-functionalresins) are simulated with embedded CNT to understand how the affinity to nanoparticles affects the mechanical response. Multiscale modeling techniques are then employed to translate the molecular phenomena observed to predict the behavior of realistic composites. The effective stiffness of hybrid composites are predicted for CNT/epoxy composites with randomly oriented CNTs, for CF/CNT/epoxy systems with aligned CFs and randomly oriented CNTs, and for woven CF/CNT/epoxy fabric with randomly oriented CNTs. The results indicate that in the CNT/epoxy systems the epoxy type has a significant influence on the elastic properties. For the CF/CNT/epoxy hybrid composites, the axial modulus is highly influenced by CF concentration, while the transverse modulus is primarily affected by the CNT weight fraction.

Development of realistic thermal hydraulic system analysis code

Energy Technology Data Exchange (ETDEWEB)

Lee, Won Jae; Chung, B. D; Kim, K. D. [and others

2002-05-01

The realistic safety analysis system is essential for nuclear safety research, advanced reactor development, safety analysis in nuclear industry and 'in-house' plant design capability development. In this project, we have developed a best-estimate multi-dimensional thermal-hydraulic system code, MARS, which is based on the integrated version of the RELAP5 and COBRA-TF codes. To improve the realistic analysis capability, we have improved the models for multi-dimensional two-phase flow phenomena and for advanced two-phase flow modeling. In addition, the GUI (Graphic User Interface) feature were developed to enhance the user's convenience. To develop the coupled analysis capability, the MARS code were linked with the three-dimensional reactor kinetics code (MASTER), the core thermal analysis code (COBRA-III/CP), and the best-estimate containment analysis code (CONTEMPT), resulting in MARS/MASTER/COBRA/CONTEMPT. Currently, the MARS code system has been distributed to 18 domestic organizations, including research, industrial, regulatory organizations and universities. The MARS has been being widely used for the safety research of existing PWRs, advanced PWR, CANDU and research reactor, the pre-test analysis of TH experiments, and others.

Development of realistic thermal hydraulic system analysis code

International Nuclear Information System (INIS)

Lee, Won Jae; Chung, B. D; Kim, K. D.

2002-05-01

The realistic safety analysis system is essential for nuclear safety research, advanced reactor development, safety analysis in nuclear industry and 'in-house' plant design capability development. In this project, we have developed a best-estimate multi-dimensional thermal-hydraulic system code, MARS, which is based on the integrated version of the RELAP5 and COBRA-TF codes. To improve the realistic analysis capability, we have improved the models for multi-dimensional two-phase flow phenomena and for advanced two-phase flow modeling. In addition, the GUI (Graphic User Interface) feature were developed to enhance the user's convenience. To develop the coupled analysis capability, the MARS code were linked with the three-dimensional reactor kinetics code (MASTER), the core thermal analysis code (COBRA-III/CP), and the best-estimate containment analysis code (CONTEMPT), resulting in MARS/MASTER/COBRA/CONTEMPT. Currently, the MARS code system has been distributed to 18 domestic organizations, including research, industrial, regulatory organizations and universities. The MARS has been being widely used for the safety research of existing PWRs, advanced PWR, CANDU and research reactor, the pre-test analysis of TH experiments, and others

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

International Nuclear Information System (INIS)

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

2005-01-01

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

Photo Realistic 3d Modeling with Uav: GEDİK Ahmet Pasha Mosque in AFYONKARAHİSAR

Science.gov (United States)

Uysal, M.; Toprak, A. S.; Polat, N.

2013-07-01

Many of the cultural heritages in the world have been totally or partly destroyed by natural events and human activities such as earthquake, flood and fire until the present day. Cultural heritages are legacy for us as well; it is also a fiduciary for next generation. To deliver this fiduciary to the future generations, cultural heritages have to be protected and registered. There are different methods for applying this registry but Photogrammetry is the most accurate and rapid method. Photogrammetry enables us to registry cultural heritages and generating 3D photo-realistic models. Nowadays, 3D models are being used in various fields such as education and tourism. In registration of complex and high construction by Photogrammetry, there are some problems in data acquisition and processing. Especially for high construction's photographs, some additional equipment is required such as balloon and lifter. In recent years The Unmanned Aerial Vehicles (UAV) are commonly started to be used in different fields for different goals. In Photogrammetry, The UAVs are being used for particularly data acquisition. It is not always easy to capture data due to the situation of historical places and their neighbourhood. The use of UAVs for documentation of cultural heritage will make an important contribution. The main goals of this study are to survey cultural heritages by Photogrammetry and to investigate the potential of UAVs in 3D modelling. In this purpose we surveyed Gedik Ahmet Pasha Mosque photogrammetricly by UAV and will produce photorealistic 3D model. Gedik Ahmet Pasha, The Grand Vizier of Fatih Sultan Mehmet, has been in Afyonkarahisar during the campaign to Karaman between the years of 1472-1473. He wanted Architect Ayaz Agha to build a complex of Bathhouse, Mosque and a Madrasah here, Afyon, due to admiration of this city. Gedik Ahmet Pasha Mosque is in the centre of this complex. Gedik Ahmet Pasha Mosque is popularly known as Imaret Mosque among the people of Afyon

PHOTO REALISTIC 3D MODELING WITH UAV: GEDİK AHMET PASHA MOSQUE IN AFYONKARAHİSAR

Directory of Open Access Journals (Sweden)

M. Uysal

2013-07-01

Full Text Available Many of the cultural heritages in the world have been totally or partly destroyed by natural events and human activities such as earthquake, flood and fire until the present day. Cultural heritages are legacy for us as well; it is also a fiduciary for next generation. To deliver this fiduciary to the future generations, cultural heritages have to be protected and registered. There are different methods for applying this registry but Photogrammetry is the most accurate and rapid method. Photogrammetry enables us to registry cultural heritages and generating 3D photo-realistic models. Nowadays, 3D models are being used in various fields such as education and tourism. In registration of complex and high construction by Photogrammetry, there are some problems in data acquisition and processing. Especially for high construction's photographs, some additional equipment is required such as balloon and lifter. In recent years The Unmanned Aerial Vehicles (UAV are commonly started to be used in different fields for different goals. In Photogrammetry, The UAVs are being used for particularly data acquisition. It is not always easy to capture data due to the situation of historical places and their neighbourhood. The use of UAVs for documentation of cultural heritage will make an important contribution. The main goals of this study are to survey cultural heritages by Photogrammetry and to investigate the potential of UAVs in 3D modelling. In this purpose we surveyed Gedik Ahmet Pasha Mosque photogrammetricly by UAV and will produce photorealistic 3D model. Gedik Ahmet Pasha, The Grand Vizier of Fatih Sultan Mehmet, has been in Afyonkarahisar during the campaign to Karaman between the years of 1472–1473. He wanted Architect Ayaz Agha to build a complex of Bathhouse, Mosque and a Madrasah here, Afyon, due to admiration of this city. Gedik Ahmet Pasha Mosque is in the centre of this complex. Gedik Ahmet Pasha Mosque is popularly known as Imaret Mosque among

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.

Multi-level molecular modelling for plasma medicine

International Nuclear Information System (INIS)

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

2016-01-01

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

Tuukka Kaidesoja on Critical Realist Transcendental Realism

Directory of Open Access Journals (Sweden)

Groff Ruth

2015-09-01

Full Text Available I argue that critical realists think pretty much what Tukka Kaidesoja says that he himself thinks, but also that Kaidesoja’s objections to the views that he attributes to critical realists are not persuasive.

Integrated multiscale modeling of molecular computing devices

International Nuclear Information System (INIS)

Cummings, Peter T; Leng Yongsheng

2005-01-01

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

Dose related risk and effect assessment model (DREAM) -- A more realistic approach to risk assessment of offshore discharges

International Nuclear Information System (INIS)

Johnsen, S.; Furuholt, E.

1995-01-01

Risk assessment of discharges from offshore oil and gas production to the marine environment features determination of potential environmental concentration (PEC) levels and no observed effect concentration (NOEC) levels. The PEC values are normally based on dilution of chemical components in the actual discharge source in the recipient, while the NOEC values are determined by applying a safety factor to acute toxic effects from laboratory tests. The DREAM concept focuses on realistic exposure doses as function of contact time and dilution, rather than fixed exposure concentrations of chemicals in long time exposure regimes. In its present state, the DREAM model is based on a number of assumptions with respect to the link between real life exposure doses and effects observed in laboratory tests. A research project has recently been initiated to develop the concept further, with special focus on chronic effects of different chemical compounds on the marine ecosystem. One of the questions that will be addressed is the link between exposure time, dose, concentration and effect. Validation of the safety factors applied for transforming acute toxic data into NOEC values will also be included. The DREAM model has been used by Statoil for risk assessment of discharges from new and existing offshore oil and gas production fields, and has been found to give a much more realistic results than conventional risk assessment tools. The presentation outlines the background for the DREAM approach, describes the model in its present state, discusses further developments and applications, and shows a number of examples on the performance of DREAM

Investigations of sensitivity and resolution of ECG and MCG in a realistically shaped thorax model

International Nuclear Information System (INIS)

Mäntynen, Ville; Konttila, Teijo; Stenroos, Matti

2014-01-01

Solving the inverse problem of electrocardiography (ECG) and magnetocardiography (MCG) is often referred to as cardiac source imaging. Spatial properties of ECG and MCG as imaging systems are, however, not well known. In this modelling study, we investigate the sensitivity and point-spread function (PSF) of ECG, MCG, and combined ECG+MCG as a function of source position and orientation, globally around the ventricles: signal topographies are modelled using a realistically-shaped volume conductor model, and the inverse problem is solved using a distributed source model and linear source estimation with minimal use of prior information. The results show that the sensitivity depends not only on the modality but also on the location and orientation of the source and that the sensitivity distribution is clearly reflected in the PSF. MCG can better characterize tangential anterior sources (with respect to the heart surface), while ECG excels with normally-oriented and posterior sources. Compared to either modality used alone, the sensitivity of combined ECG+MCG is less dependent on source orientation per source location, leading to better source estimates. Thus, for maximal sensitivity and optimal source estimation, the electric and magnetic measurements should be combined. (paper)

Realistic Paleobathymetry of the Cenomanian–Turonian (94 Ma Boundary Global Ocean

Directory of Open Access Journals (Sweden)

Arghya Goswami

2018-01-01

Full Text Available At present, global paleoclimate simulations are prepared with bathtub-like, flat, featureless and steep walled ocean bathymetry, which is neither realistic nor suitable. In this article, we present the first enhanced version of a reconstructed paleobathymetry for Cenomanian–Turonian (94 Ma time in a 0.1° × 0.1° resolution, that is both realistic and suitable for use in paleo-climate studies. This reconstruction is an extrapolation of a parameterized modern ocean bathymetry that combines simple geophysical models (standard plate cooling model for the oceanic lithosphere based on ocean crustal age, global modern oceanic sediment thicknesses, and generalized shelf-slope-rise structures calibrated from a published global relief model of the modern world (ETOPO1 at active and passive continental margins. The base version of this Cenomanian–Turonian paleobathymetry reconstruction is then updated with known submarine large igneous provinces, plateaus, and seamounts to minimize the difference between the reconstructed paleobathymetry and the real bathymetry that once existed.

Realistic terrain visualization based on 3D virtual world technology

Science.gov (United States)

Huang, Fengru; Lin, Hui; Chen, Bin; Xiao, Cai

2010-11-01

The rapid advances in information technologies, e.g., network, graphics processing, and virtual world, have provided challenges and opportunities for new capabilities in information systems, Internet applications, and virtual geographic environments, especially geographic visualization and collaboration. In order to achieve meaningful geographic capabilities, we need to explore and understand how these technologies can be used to construct virtual geographic environments to help to engage geographic research. The generation of three-dimensional (3D) terrain plays an important part in geographical visualization, computer simulation, and virtual geographic environment applications. The paper introduces concepts and technologies of virtual worlds and virtual geographic environments, explores integration of realistic terrain and other geographic objects and phenomena of natural geographic environment based on SL/OpenSim virtual world technologies. Realistic 3D terrain visualization is a foundation of construction of a mirror world or a sand box model of the earth landscape and geographic environment. The capabilities of interaction and collaboration on geographic information are discussed as well. Further virtual geographic applications can be developed based on the foundation work of realistic terrain visualization in virtual environments.

Realistic Simulations of Coronagraphic Observations with WFIRST

Science.gov (United States)

Rizzo, Maxime; Zimmerman, Neil; Roberge, Aki; Lincowski, Andrew; Arney, Giada; Stark, Chris; Jansen, Tiffany; Turnbull, Margaret; WFIRST Science Investigation Team (Turnbull)

2018-01-01

We present a framework to simulate observing scenarios with the WFIRST Coronagraphic Instrument (CGI). The Coronagraph and Rapid Imaging Spectrograph in Python (crispy) is an open-source package that can be used to create CGI data products for analysis and development of post-processing routines. The software convolves time-varying coronagraphic PSFs with realistic astrophysical scenes which contain a planetary architecture, a consistent dust structure, and a background field composed of stars and galaxies. The focal plane can be read out by a WFIRST electron-multiplying CCD model directly, or passed through a WFIRST integral field spectrograph model first. Several elementary post-processing routines are provided as part of the package.

Understanding molecular motor walking along a microtubule: a themosensitive asymmetric Brownian motor driven by bubble formation.

Science.gov (United States)

Arai, Noriyoshi; Yasuoka, Kenji; Koishi, Takahiro; Ebisuzaki, Toshikazu; Zeng, Xiao Cheng

2013-06-12

The "asymmetric Brownian ratchet model", a variation of Feynman's ratchet and pawl system, is invoked to understand the kinesin walking behavior along a microtubule. The model system, consisting of a motor and a rail, can exhibit two distinct binding states, namely, the random Brownian state and the asymmetric potential state. When the system is transformed back and forth between the two states, the motor can be driven to "walk" in one direction. Previously, we suggested a fundamental mechanism, that is, bubble formation in a nanosized channel surrounded by hydrophobic atoms, to explain the transition between the two states. In this study, we propose a more realistic and viable switching method in our computer simulation of molecular motor walking. Specifically, we propose a thermosensitive polymer model with which the transition between the two states can be controlled by temperature pulses. Based on this new motor system, the stepping size and stepping time of the motor can be recorded. Remarkably, the "walking" behavior observed in the newly proposed model resembles that of the realistic motor protein. The bubble formation based motor not only can be highly efficient but also offers new insights into the physical mechanism of realistic biomolecule motors.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Investigation of realistic PET simulations incorporating tumor patient's specificity using anthropomorphic models: Creation of an oncology database

International Nuclear Information System (INIS)

Papadimitroulas, Panagiotis; Efthimiou, Nikos; Nikiforidis, George C.; Kagadis, George C.; Loudos, George; Le Maitre, Amandine; Hatt, Mathieu; Tixier, Florent; Visvikis, Dimitris

2013-01-01

Purpose: The GATE Monte Carlo simulation toolkit is used for the implementation of realistic PET simulations incorporating tumor heterogeneous activity distributions. The reconstructed patient images include noise from the acquisition process, imaging system's performance restrictions and have limited spatial resolution. For those reasons, the measured intensity cannot be simply introduced in GATE simulations, to reproduce clinical data. Investigation of the heterogeneity distribution within tumors applying partial volume correction (PVC) algorithms was assessed. The purpose of the present study was to create a simulated oncology database based on clinical data with realistic intratumor uptake heterogeneity properties.Methods: PET/CT data of seven oncology patients were used in order to create a realistic tumor database investigating the heterogeneity activity distribution of the simulated tumors. The anthropomorphic models (NURBS based cardiac torso and Zubal phantoms) were adapted to the CT data of each patient, and the activity distribution was extracted from the respective PET data. The patient-specific models were simulated with the Monte Carlo Geant4 application for tomography emission (GATE) in three different levels for each case: (a) using homogeneous activity within the tumor, (b) using heterogeneous activity distribution in every voxel within the tumor as it was extracted from the PET image, and (c) using heterogeneous activity distribution corresponding to the clinical image following PVC. The three different types of simulated data in each case were reconstructed with two iterations and filtered with a 3D Gaussian postfilter, in order to simulate the intratumor heterogeneous uptake. Heterogeneity in all generated images was quantified using textural feature derived parameters in 3D according to the ground truth of the simulation, and compared to clinical measurements. Finally, profiles were plotted in central slices of the tumors, across lines with

Generating realistic roofs over a rectilinear polygon

KAUST Repository

Ahn, Heekap

2011-01-01

Given a simple rectilinear polygon P in the xy-plane, a roof over P is a terrain over P whose faces are supported by planes through edges of P that make a dihedral angle π/4 with the xy-plane. In this paper, we introduce realistic roofs by imposing a few additional constraints. We investigate the geometric and combinatorial properties of realistic roofs, and show a connection with the straight skeleton of P. We show that the maximum possible number of distinct realistic roofs over P is ( ⌊(n-4)/4⌋ (n-4)/2) when P has n vertices. We present an algorithm that enumerates a combinatorial representation of each such roof in O(1) time per roof without repetition, after O(n 4) preprocessing time. We also present an O(n 5)-time algorithm for computing a realistic roof with minimum height or volume. © 2011 Springer-Verlag.

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.

Computational investigation of nonlinear microwave tomography on anatomically realistic breast phantoms

DEFF Research Database (Denmark)

Jensen, P. D.; Rubæk, Tonny; Mohr, J. J.

2013-01-01

The performance of a nonlinear microwave tomography algorithm is tested using simulated data from anatomically realistic breast phantoms. These tests include several different anatomically correct breast models from the University of Wisconsin-Madison repository with and without tumors inserted....

Detailed performance analysis of realistic solar photovoltaic systems at extensive climatic conditions

International Nuclear Information System (INIS)

Gupta, Ankit; Chauhan, Yogesh K.

2016-01-01

In recent years, solar energy has been considered as one of the principle renewable energy source for electric power generation. In this paper, single diode photovoltaic (PV) system and double/bypass diode based PV system are designed in MATLAB/Simulink environment based on their mathematical modeling and are validated with a commercially available solar panel. The novelty of the paper is to include the effect of climatic conditions i.e. variable irradiation level, wind speed, temperature, humidity level and dust accumulation in the modeling of both the PV systems to represent a realistic PV system. The comprehensive investigations are made on both the modeled PV systems. The obtained results show the satisfactory performance for realistic models of the PV system. Furthermore, an in depth comparative analysis is carried out for both PV systems. - Highlights: • Modeling of Single diode and Double diode PV systems in MATLAB/Simulink software. • Validation of designed PV systems with a commercially available PV panel. • Acquisition and employment of key climatic factors in modeling of the PV systems. • Evaluation of main model parameters of both the PV systems. • Detailed comparative assessment of both the modeled PV system parameters.

Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics

Science.gov (United States)

Tortora, Maxime M. C.; Doye, Jonathan P. K.

2017-12-01

We detail the application of bounding volume hierarchies to accelerate second-virial evaluations for arbitrary complex particles interacting through hard and soft finite-range potentials. This procedure, based on the construction of neighbour lists through the combined use of recursive atom-decomposition techniques and binary overlap search schemes, is shown to scale sub-logarithmically with particle resolution in the case of molecular systems with high aspect ratios. Its implementation within an efficient numerical and theoretical framework based on classical density functional theory enables us to investigate the cholesteric self-assembly of a wide range of experimentally relevant particle models. We illustrate the method through the determination of the cholesteric behavior of hard, structurally resolved twisted cuboids, and report quantitative evidence of the long-predicted phase handedness inversion with increasing particle thread angles near the phenomenological threshold value of 45°. Our results further highlight the complex relationship between microscopic structure and helical twisting power in such model systems, which may be attributed to subtle geometric variations of their chiral excluded-volume manifold.

Bayesian inversion using a geologically realistic and discrete model space

Science.gov (United States)

Jaeggli, C.; Julien, S.; Renard, P.

2017-12-01

Since the early days of groundwater modeling, inverse methods play a crucial role. Many research and engineering groups aim to infer extensive knowledge of aquifer parameters from a sparse set of observations. Despite decades of dedicated research on this topic, there are still several major issues to be solved. In the hydrogeological framework, one is often confronted with underground structures that present very sharp contrasts of geophysical properties. In particular, subsoil structures such as karst conduits, channels, faults, or lenses, strongly influence groundwater flow and transport behavior of the underground. For this reason it can be essential to identify their location and shape very precisely. Unfortunately, when inverse methods are specially trained to consider such complex features, their computation effort often becomes unaffordably high. The following work is an attempt to solve this dilemma. We present a new method that is, in some sense, a compromise between the ergodicity of Markov chain Monte Carlo (McMC) methods and the efficient handling of data by the ensemble based Kalmann filters. The realistic and complex random fields are generated by a Multiple-Point Statistics (MPS) tool. Nonetheless, it is applicable with any conditional geostatistical simulation tool. Furthermore, the algorithm is independent of any parametrization what becomes most important when two parametric systems are equivalent (permeability and resistivity, speed and slowness, etc.). When compared to two existing McMC schemes, the computational effort was divided by a factor of 12.

Realistic electricity market simulator for energy and economic studies

International Nuclear Information System (INIS)

Bernal-Agustin, Jose L.; Contreras, Javier; Conejo, Antonio J.; Martin-Flores, Raul

2007-01-01

Electricity market simulators have become a useful tool to train engineers in the power industry. With the maturing of electricity markets throughout the world, there is a need for sophisticated software tools that can replicate the actual behavior of power markets. In most of these markets, power producers/consumers submit production/demand bids and the Market Operator clears the market producing a single price per hour. What makes markets different from each other are the bidding rules and the clearing algorithms to balance the market. This paper presents a realistic simulator of the day-ahead electricity market of mainland Spain. All the rules that govern this market are modeled. This simulator can be used either to train employees by power companies or to teach electricity markets courses in universities. To illustrate the tool, several realistic case studies are presented and discussed. (author)

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...

Kuhn: Realist or Antirealist?

Directory of Open Access Journals (Sweden)

Michel Ghins

1998-06-01

Full Text Available Although Kuhn is much more an antirealist than a realist, the earlier and later articulations of realist and antirealist ingredients in his views merit close scrutiny. What are the constituents of the real invariant World posited by Kuhn and its relation to the mutable paradigm-related worlds? Various proposed solutions to this problem (dubbed the "new-world problem" by Ian Hacking are examined and shown to be unsatisfactory. In The Structure of Scientific Revolutions, the stable World can reasonably be taken to be made up of ordinary perceived objects, whereas in Kuhn's later works the transparadigmatic World is identified with something akin to the Kantian world-in-itself. It is argued that both proposals are beset with insuperable difficulties which render Kuhn's earlier and later versions of antirealism implausible.

Empirical Evidence for Niss' "Implemented Anticipation" in Mathematising Realistic Situations

Science.gov (United States)

Stillman, Gloria; Brown, Jill P.

2012-01-01

Mathematisation of realistic situations is an on-going focus of research. Classroom data from a Year 9 class participating in a program of structured modelling of real situations was analysed for evidence of Niss's theoretical construct, implemented anticipation, during mathematisation. Evidence was found for two of three proposed aspects. In…

Realistic microscopic level densities for spherical nuclei

International Nuclear Information System (INIS)

Cerf, N.

1994-01-01

Nuclear level densities play an important role in nuclear reactions such as the formation of the compound nucleus. We develop a microscopic calculation of the level density based on a combinatorial evaluation from a realistic single-particle level scheme. This calculation makes use of a fast Monte Carlo algorithm allowing us to consider large shell model spaces which could not be treated previously in combinatorial approaches. Since our model relies on a microscopic basis, it can be applied to exotic nuclei with more confidence than the commonly used semiphenomenological formuals. An exhaustive comparison of our predicted neutron s-wave resonance spacings with experimental data for a wide range of nuclei is presented

A Local Realistic Reconciliation of the EPR Paradox

Science.gov (United States)

Sanctuary, Bryan

2014-03-01

The exact violation of Bell's Inequalities is obtained with a local realistic model for spin. The model treats one particle that comprises a quantum ensemble and simulates the EPR data one coincidence at a time as a product state. Such a spin is represented by operators σx , iσy ,σz in its body frame rather than the usual set of σX ,σY ,σZ in the laboratory frame. This model, assumed valid in the absence of a measuring probe, contains both quantum polarizations and coherences. Each carries half the EPR correlation, but only half can be measured using coincidence techniques. The model further predicts the filter angles that maximize the spin correlation in EPR experiments.

Stroke type differentiation using spectrally constrained multifrequency EIT: evaluation of feasibility in a realistic head model

International Nuclear Information System (INIS)

Malone, Emma; Jehl, Markus; Arridge, Simon; Betcke, Timo; Holder, David

2014-01-01

We investigate the application of multifrequency electrical impedance tomography (MFEIT) to imaging the brain in stroke patients. The use of MFEIT could enable early diagnosis and thrombolysis of ischaemic stroke, and therefore improve the outcome of treatment. Recent advances in the imaging methodology suggest that the use of spectral constraints could allow for the reconstruction of a one-shot image. We performed a simulation study to investigate the feasibility of imaging stroke in a head model with realistic conductivities. We introduced increasing levels of modelling errors to test the robustness of the method to the most common sources of artefact. We considered the case of errors in the electrode placement, spectral constraints, and contact impedance. The results indicate that errors in the position and shape of the electrodes can affect image quality, although our imaging method was successful in identifying tissues with sufficiently distinct spectra. (paper)

Effects of Organics on the Adsorption and Mobility of Metal Cations in Clay Systems: Computational Molecular Modeling Approach

International Nuclear Information System (INIS)

Kalinichev, Andrey G.; Ngouana Wakou, Brice F.; Loganathan, Narasimhan

2013-01-01

Understanding and prediction of many natural and anthropogenic environmental processes ultimately depend on a fundamental understanding of the chemistry occurring at the mineral-fluid inter-faces. Clay-related minerals and natural organic matter (NOM) are ubiquitous in the environment, and metal-NOM complexation induces strong correlations between the NOM concentration in water and the capacity of clay particles to bind metals, thus affecting their speciation, solubility and toxicity in the environment. Despite significant geochemical, environmental and technological interest, the molecular-level mechanisms and dynamics of the physical and chemical processes involving NOM are not yet well understood. In this presentation we compare three different molecular dynamics (MD) computer simulations of metal-NOM complexation in aqueous solutions. The simulation results indicate that despite some obvious quantitative variations in the computed values depending on the size of the simulated system and on the parameters of the force field models used, all three simulations are quite robust and consistent. In particular, approximately 35-50% of Ca 2+ ions in all simulations are associated with the carboxylic groups of NOM at near-neutral pH. The stability of bidentate-coordinated contact ion pair complexes is also always strongly preferred. Easy association of metal cations with negatively charged NOM functional groups and negatively charged clay surfaces allows us to predict that cationic bridging could be the most probable mechanism of NOM association with clays in natural environments. New MD simulations are currently in progress to quantitatively assess these predictions on a molecular scale for nuclear waste disposal applications. New larger-scale clay models incorporate a more realistic representation of the structural and compositional disorder of natural illites and smectites and employ CLAYFF - a fully flexible general force field suitable for the molecular simulations

Molecular Dynamics Modeling of Carbon Nanotube Composite Fracture Using ReaxFF

Science.gov (United States)

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

2016-01-01

Carbon nanotube (CNT) fiber reinforced composites with specific tensile strengths and moduli approaching those of aerospace grade carbon fiber composites have recently been reported. This achievement was enabled by the emerging availability of high N/tex yarns in kilometer-scale quantities. While the production of this yarn is an impressive advance, its strength is still much lower than that of the individual CNTs comprising the yarn. Closing this gap requires understanding load transfer between CNTs at the nanometer dimensional scale. This work uses reactive molecular dynamics simulations to gain an understanding at the nanometer scale of the key factors that determine CNT nanocomposite mechanical performance, and to place more realistic upper bounds on the target properties. While molecular dynamics simulations using conventional force fields can predict elastic properties, the ReaxFF reactive forcefield can also model fracture behavior because of its ability to accurately describe bond breaking and formation during a simulation. The upper and lower bounds of CNT composite properties are investigated by comparing systems composed of CNTs continuously connected across the periodic boundary with systems composed of finite length CNTs. These lengths, effectively infinite for the continuous tubes and an aspect ratio of 13 for the finite length case, result from practical limitations on the number of atoms that can be included in a simulation. Experimentally measured aspect ratios are typically on the order of 100,000, so the calculated results should represent upper and lower limits on experimental mechanical properties. Finally, the effect of various degrees of covalent crosslinking between the CNTs and amorphous carbon matrix is considered to identify the amount of CNT-matrix covalent bonding that maximizes overall composite properties.

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

CERN Document Server

Ji, Sungchul

2012-01-01

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

Rational versus Emotional Reasoning in a Realistic Multi-Objective Environment

OpenAIRE

Mayboudi, Seyed Mohammad Hossein

2011-01-01

ABSTRACT: Emotional intelligence and its associated with models have recently become one of new active studies in the field of artificial intelligence. Several works have been performed on modelling of emotional behaviours such as love, hate, happiness and sadness. This study presents a comparative evaluation of rational and emotional behaviours and the effects of emotions on the decision making process of agents in a realistic multi-objective environment. NetLogo simulation environment is u...

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

International Nuclear Information System (INIS)

Khorasani, R.; Pourmahdian, S.

2007-01-01

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

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.

Complete methodology on generating realistic wind speed profiles based on measurements

DEFF Research Database (Denmark)

Gavriluta, Catalin; Spataru, Sergiu; Mosincat, Ioan

2012-01-01

, wind modelling for medium and large time scales is poorly treated in the present literature. This paper presents methods for generating realistic wind speed profiles based on real measurements. The wind speed profile is divided in a low- frequency component (describing long term variations...

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

Science.gov (United States)

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

2017-06-28

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

Downscaling Ocean Conditions: Initial Results using a Quasigeostrophic and Realistic Ocean Model

Science.gov (United States)

Katavouta, Anna; Thompson, Keith

2014-05-01

Previous theoretical work (Henshaw et al, 2003) has shown that the small-scale modes of variability of solutions of the unforced, incompressible Navier-Stokes equation, and Burgers' equation, can be reconstructed with surprisingly high accuracy from the time history of a few of the large-scale modes. Motivated by this theoretical work we first describe a straightforward method for assimilating information on the large scales in order to recover the small scale oceanic variability. The method is based on nudging in specific wavebands and frequencies and is similar to the so-called spectral nudging method that has been used successfully for atmospheric downscaling with limited area models (e.g. von Storch et al., 2000). The validity of the method is tested using a quasigestrophic model configured to simulate a double ocean gyre separated by an unstable mid-ocean jet. It is shown that important features of the ocean circulation including the position of the meandering mid-ocean jet and associated pinch-off eddies can indeed be recovered from the time history of a small number of large-scales modes. The benefit of assimilating additional time series of observations from a limited number of locations, that alone are too sparse to significantly improve the recovery of the small scales using traditional assimilation techniques, is also demonstrated using several twin experiments. The final part of the study outlines the application of the approach using a realistic high resolution (1/36 degree) model, based on the NEMO (Nucleus for European Modelling of the Ocean) modeling framework, configured for the Scotian Shelf of the east coast of Canada. The large scale conditions used in this application are obtained from the HYCOM (HYbrid Coordinate Ocean Model) + NCODA (Navy Coupled Ocean Data Assimilation) global 1/12 degree analysis product. Henshaw, W., Kreiss, H.-O., Ystrom, J., 2003. Numerical experiments on the interaction between the larger- and the small-scale motion of

Exophobic Quasi-Realistic Heterotic String Vacua

CERN Document Server

Assel, Benjamin; Faraggi, Alon E; Kounnas, Costas; Rizos, John

2009-01-01

We demonstrate the existence of heterotic-string vacua that are free of massless exotic fields. The need to break the non-Abelian GUT symmetries in k=1 heterotic-string models by Wilson lines, while preserving the GUT embedding of the weak-hypercharge and the GUT prediction sin^2\\theta_w(M(GUT))=3/8, necessarily implies that the models contain states with fractional electric charge. Such states are severely restricted by observations, and must be confined or sufficiently massive and diluted. We construct the first quasi-realistic heterotic-string models in which the exotic states do not appear in the massless spectrum, and only exist, as they must, in the massive spectrum. The SO(10) GUT symmetry is broken to the Pati-Salam subgroup. Our PS heterotic-string models contain adequate Higgs representations to break the GUT and electroweak symmetry, as well as colour Higgs triplets that can be used for the missing partner mechanism. By statistically sampling the space of Pati-Salam vacua we demonstrate the abundan...

Creating photo-realistic works in a 3D scene using layers styles to create an animation

Science.gov (United States)

Avramescu, A. M.

2015-11-01

Creating realist objects in a 3D scene is not an easy work. We have to be very careful to make the creation very detailed. If we don't know how to make these photo-realistic works, by using the techniques and a good reference photo we can create an amazing amount of detail and realism. For example, in this article there are some of these detailed methods from which we can learn the techniques necessary to make beautiful and realistic objects in a scene. More precisely, in this paper, we present how to create a 3D animated scene, mainly using the Pen Tool and Blending Options. Indeed, this work is based on teaching some simple ways of using the Layer Styles to create some great shadows, lights, textures and a realistic sense of 3 Dimension. The present work involves also showing how some interesting ways of using the illuminating and rendering options can create a realistic effect in a scene. Moreover, this article shows how to create photo realistic 3D models from a digital image. The present work proposes to present how to use Illustrator paths, texturing, basic lighting and rendering, how to apply textures and how to parent the building and objects components. We also propose to use this proposition to recreate smaller details or 3D objects from a 2D image. After a critic art stage, we are able now to present in this paper the architecture of a design method that proposes to create an animation. The aim is to create a conceptual and methodological tutorial to address this issue both scientifically and in practice. This objective also includes proposing, on strong scientific basis, a model that gives the possibility of a better understanding of the techniques necessary to create a realistic animation.

Development of a Shipboard Remote Control and Telemetry Experimental System for Large-Scale Model's Motions and Loads Measurement in Realistic Sea Waves.

Science.gov (United States)

Jiao, Jialong; Ren, Huilong; Adenya, Christiaan Adika; Chen, Chaohe

2017-10-29

Wave-induced motion and load responses are important criteria for ship performance evaluation. Physical experiments have long been an indispensable tool in the predictions of ship's navigation state, speed, motions, accelerations, sectional loads and wave impact pressure. Currently, majority of the experiments are conducted in laboratory tank environment, where the wave environments are different from the realistic sea waves. In this paper, a laboratory tank testing system for ship motions and loads measurement is reviewed and reported first. Then, a novel large-scale model measurement technique is developed based on the laboratory testing foundations to obtain accurate motion and load responses of ships in realistic sea conditions. For this purpose, a suite of advanced remote control and telemetry experimental system was developed in-house to allow for the implementation of large-scale model seakeeping measurement at sea. The experimental system includes a series of technique sensors, e.g., the Global Position System/Inertial Navigation System (GPS/INS) module, course top, optical fiber sensors, strain gauges, pressure sensors and accelerometers. The developed measurement system was tested by field experiments in coastal seas, which indicates that the proposed large-scale model testing scheme is capable and feasible. Meaningful data including ocean environment parameters, ship navigation state, motions and loads were obtained through the sea trial campaign.

Realistic Simulation of Rice Plant

Directory of Open Access Journals (Sweden)

Wei-long DING

2011-09-01

Full Text Available The existing research results of virtual modeling of rice plant, however, is far from perfect compared to that of other crops due to its complex structure and growth process. Techniques to visually simulate the architecture of rice plant and its growth process are presented based on the analysis of the morphological characteristics at different stages. Firstly, the simulations of geometrical shape, the bending status and the structural distortion of rice leaves are conducted. Then, by using an improved model for bending deformation, the curved patterns of panicle axis and various types of panicle branches are generated, and the spatial shape of rice panicle is therefore created. Parametric L-system is employed to generate its topological structures, and finite-state automaton is adopted to describe the development of geometrical structures. Finally, the computer visualization of three-dimensional morphologies of rice plant at both organ and individual levels is achieved. The experimental results showed that the proposed methods of modeling the three-dimensional shapes of organs and simulating the growth of rice plant are feasible and effective, and the generated three-dimensional images are realistic.

Constructing Molecular Models with Low-Cost Toy Beads

Science.gov (United States)

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

2012-01-01

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

Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

KAUST Repository

Kadoura, Ahmad Salim

2016-01-01

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

Absorption of airborne molecular iodine by water sprays

International Nuclear Information System (INIS)

Albert, M.F.; Wichner, R.P.; Baumgarten, P.K.

1986-01-01

A computer model, I2WASH, which accounts for the effect of hydrolysis reactions between molecular iodine and water, has been developed to predict the rate of removal of gaseous molecular iodine by water sprays. It has been shown that the hydrolysis reactions can affect the concentration driving force of mass transfer for molecular iodine absorption. Thus, factors that affect the hydrolysis kinetics, such as spray solution pH, iodine concentration, and temperature, should be considered in the design of a well-based absorption model. The described model also includes the effects of spray drop-size distribution, convective heat transfer, droplet evaporation or water condensation, decay heating, and ventilation air flow through the containment. The model was originally developed at Oak Ridge National Laboratory (ORNL) in 1985 for the Nuclear Regulatory Commission's Severe Accident Sequence Analysis program and has been improved to assist in a comprehensive probability risk assessment of the Savannah River Plant (SRP). Results obtained using the model are compared with those of the Containment Systems Experiments conducted at Pacific Northwest Laboratories (PNL) in 1970. An improvement over the earlier model is indicated at room temperatures, but accuracy decreases as the temperature rises. The decreased agreement at high temperature is partially due to an incomplete knowledge of the temperature effects on iodine hydrolysis reactions. The results of the I2WASH model for a postulated catastrophic accident at SRP show that ∼85% of the molecular iodine will be captured by the sprays at a buffered pH of 10.0, and ∼52% will be captured at a buffered pH of 7.0. The model is believed to be a significant improvement over (and more realistic than) other models

A realistic pattern of fermion masses from a five-dimensional SO(10) model

International Nuclear Information System (INIS)

Feruglio, Ferruccio; Patel, Ketan M.; Vicino, Denise

2015-01-01

We provide a unified description of fermion masses and mixing angles in the framework of a supersymmetric grand unified SO(10) model with anarchic Yukawa couplings of order unity. The space-time is five dimensional and the extra flat spatial dimension is compactified on the orbifold S 1 /(Z 2 ×Z 2 ′ ), leading to Pati-Salam gauge symmetry on the boundary where Yukawa interactions are localised. The gauge symmetry breaking is completed by means of a rather economic scalar sector, avoiding the doublet-triplet splitting problem. The matter fields live in the bulk and their massless modes get exponential profiles, which naturally explain the mass hierarchy of the different fermion generations. Quarks and leptons properties are naturally reproduced by a mechanism, first proposed by Kitano and Li, that lifts the SO(10) degeneracy of bulk masses in terms of a single parameter. The model provides a realistic pattern of fermion masses and mixing angles for large values of tan β. It favours normally ordered neutrino mass spectrum with the lightest neutrino mass below 0.01 eV and no preference for leptonic CP violating phases. The right handed neutrino mass spectrum is very hierarchical and does not allow for thermal leptogenesis. We analyse several variants of the basic framework and find that the results concerning the fermion spectrum are remarkably stable.

Adapting realist synthesis methodology: The case of workplace harassment interventions.

Science.gov (United States)

Carr, Tracey; Quinlan, Elizabeth; Robertson, Susan; Gerrard, Angie

2017-12-01

Realist synthesis techniques can be used to assess complex interventions by extracting and synthesizing configurations of contexts, mechanisms, and outcomes found in the literature. Our novel and multi-pronged approach to the realist synthesis of workplace harassment interventions describes our pursuit of theory to link macro and program level theories. After discovering the limitations of a dogmatic approach to realist synthesis, we adapted our search strategy and focused our analysis on a subset of data. We tailored our realist synthesis to understand how, why, and under what circumstances workplace harassment interventions are effective. The result was a conceptual framework to test our theory-based interventions and provide the basis for subsequent realist evaluation. Our experience documented in this article contributes to an understanding of how, under what circumstances, and with what consequences realist synthesis principles can be customized. Copyright © 2017 John Wiley & Sons, Ltd.

Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

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

1992-01-01

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

Software phantom with realistic speckle modeling for validation of image analysis methods in echocardiography

Science.gov (United States)

Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten

2014-03-01

Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.

Turbulent transport measurements in a cold model of GT-burner at realistic flow rates

Directory of Open Access Journals (Sweden)

Gobyzov Oleg

2016-01-01

Full Text Available In the present work simultaneous velocity field and passive admixture concentration field measurements at realistic flow-rates conditions in a non-reacting flow in a model of combustion chamber with an industrial mixing device are reported. In the experiments for safety reasons the real fuel (natural gas was replaced with neon gas to simulate stratification in a strongly swirling flow. Measurements were performed by means of planar laser-induced fluorescence (PLIF and particle image velocimetry technique (PIV at Reynolds number, based on the mean flow rate and nozzle diameter, ≈300 000. Details on experimental technique, features of the experimental setup, images and data preprocessing procedures and results of performed measurements are given in the paper. In addition to the raw velocity and admixture concentration data in-depth evaluation approaches aimed for estimation of turbulent kinetic energy (TKE components, assessment of turbulent Schmidt number and analysis of the gradient closure hypothesis from experimental data are presented in the paper.

The independent molecular interaction sites model. Pt. 1

International Nuclear Information System (INIS)

Naumann, K.H.; Lippert, E.

1981-01-01

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

3D Realistic Radiative Hydrodynamic Modeling of a Moderate-Mass Star: Effects of Rotation

Science.gov (United States)

Kitiashvili, Irina; Kosovichev, Alexander G.; Mansour, Nagi N.; Wray, Alan A.

2018-01-01

Recent progress in stellar observations opens new perspectives in understanding stellar evolution and structure. However, complex interactions in the turbulent radiating plasma together with effects of magnetic fields and rotation make inferences of stellar properties uncertain. The standard 1D mixing-length-based evolutionary models are not able to capture many physical processes of stellar interior dynamics, but they provide an initial approximation of the stellar structure that can be used to initialize 3D time-dependent radiative hydrodynamics simulations, based on first physical principles, that take into account the effects of turbulence, radiation, and others. In this presentation we will show simulation results from a 3D realistic modeling of an F-type main-sequence star with mass 1.47 Msun, in which the computational domain includes the upper layers of the radiation zone, the entire convection zone, and the photosphere. The simulation results provide new insight into the formation and properties of the convective overshoot region, the dynamics of the near-surface, highly turbulent layer, the structure and dynamics of granulation, and the excitation of acoustic and gravity oscillations. We will discuss the thermodynamic structure, oscillations, and effects of rotation on the dynamics of the star across these layers.

Realist synthesis: illustrating the method for implementation research

Directory of Open Access Journals (Sweden)

Rycroft-Malone Jo

2012-04-01

Full Text Available Abstract Background Realist synthesis is an increasingly popular approach to the review and synthesis of evidence, which focuses on understanding the mechanisms by which an intervention works (or not. There are few published examples of realist synthesis. This paper therefore fills a gap by describing, in detail, the process used for a realist review and synthesis to answer the question ‘what interventions and strategies are effective in enabling evidence-informed healthcare?’ The strengths and challenges of conducting realist review are also considered. Methods The realist approach involves identifying underlying causal mechanisms and exploring how they work under what conditions. The stages of this review included: defining the scope of the review (concept mining and framework formulation; searching for and scrutinising the evidence; extracting and synthesising the evidence; and developing the narrative, including hypotheses. Results Based on key terms and concepts related to various interventions to promote evidence-informed healthcare, we developed an outcome-focused theoretical framework. Questions were tailored for each of four theory/intervention areas within the theoretical framework and were used to guide development of a review and data extraction process. The search for literature within our first theory area, change agency, was executed and the screening procedure resulted in inclusion of 52 papers. Using the questions relevant to this theory area, data were extracted by one reviewer and validated by a second reviewer. Synthesis involved organisation of extracted data into evidence tables, theming and formulation of chains of inference, linking between the chains of inference, and hypothesis formulation. The narrative was developed around the hypotheses generated within the change agency theory area. Conclusions Realist synthesis lends itself to the review of complex interventions because it accounts for context as well as

Sotsialistlik realist Keskküla

Index Scriptorium Estoniae

1998-01-01

Londonis 1998. a. ilmunud inglise kunstikriitiku Matthew Cullerne Bowni monograafias "Socialist Realist Painting" on eesti kunstnikest Enn Põldroos, Nikolai Kormashov, Ando Keskküla, Kormashovi ja Keskküla maalide reproduktsioonid

Molecular modeling of inorganic compounds

National Research Council Canada - National Science Library

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

2009-01-01

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

Agent-Based Modeling in Molecular Systems Biology.

Science.gov (United States)

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-06-08

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

Are there realistically interpretable local theories?

International Nuclear Information System (INIS)

d'Espagnat, B.

1989-01-01

Although it rests on strongly established proofs, the statement that no realistically interpretable local theory is compatible with some experimentally testable predictions of quantum mechanics seems at first sight to be incompatible with a few general ideas and clear-cut statements occurring in recent theoretical work by Griffiths, Omnes, and Ballentine and Jarrett. It is shown here that in fact none of the developments due to these authors can be considered as a realistically interpretable local theory, so that there is no valid reason for suspecting that the existing proofs of the statement in question are all flawed

Realistic Real-Time Outdoor Rendering in Augmented Reality

Science.gov (United States)

Kolivand, Hoshang; Sunar, Mohd Shahrizal

2014-01-01

Realistic rendering techniques of outdoor Augmented Reality (AR) has been an attractive topic since the last two decades considering the sizeable amount of publications in computer graphics. Realistic virtual objects in outdoor rendering AR systems require sophisticated effects such as: shadows, daylight and interactions between sky colours and virtual as well as real objects. A few realistic rendering techniques have been designed to overcome this obstacle, most of which are related to non real-time rendering. However, the problem still remains, especially in outdoor rendering. This paper proposed a much newer, unique technique to achieve realistic real-time outdoor rendering, while taking into account the interaction between sky colours and objects in AR systems with respect to shadows in any specific location, date and time. This approach involves three main phases, which cover different outdoor AR rendering requirements. Firstly, sky colour was generated with respect to the position of the sun. Second step involves the shadow generation algorithm, Z-Partitioning: Gaussian and Fog Shadow Maps (Z-GaF Shadow Maps). Lastly, a technique to integrate sky colours and shadows through its effects on virtual objects in the AR system, is introduced. The experimental results reveal that the proposed technique has significantly improved the realism of real-time outdoor AR rendering, thus solving the problem of realistic AR systems. PMID:25268480

Realistic real-time outdoor rendering in augmented reality.

Directory of Open Access Journals (Sweden)

Hoshang Kolivand

Full Text Available Realistic rendering techniques of outdoor Augmented Reality (AR has been an attractive topic since the last two decades considering the sizeable amount of publications in computer graphics. Realistic virtual objects in outdoor rendering AR systems require sophisticated effects such as: shadows, daylight and interactions between sky colours and virtual as well as real objects. A few realistic rendering techniques have been designed to overcome this obstacle, most of which are related to non real-time rendering. However, the problem still remains, especially in outdoor rendering. This paper proposed a much newer, unique technique to achieve realistic real-time outdoor rendering, while taking into account the interaction between sky colours and objects in AR systems with respect to shadows in any specific location, date and time. This approach involves three main phases, which cover different outdoor AR rendering requirements. Firstly, sky colour was generated with respect to the position of the sun. Second step involves the shadow generation algorithm, Z-Partitioning: Gaussian and Fog Shadow Maps (Z-GaF Shadow Maps. Lastly, a technique to integrate sky colours and shadows through its effects on virtual objects in the AR system, is introduced. The experimental results reveal that the proposed technique has significantly improved the realism of real-time outdoor AR rendering, thus solving the problem of realistic AR systems.

Generating realistic images using Kray

Science.gov (United States)

Tanski, Grzegorz

2004-07-01

Kray is an application for creating realistic images. It is written in C++ programming language, has a text-based interface, solves global illumination problem using techniques such as radiosity, path tracing and photon mapping.

Investigation of realistic PET simulations incorporating tumor patient's specificity using anthropomorphic models: Creation of an oncology database

Energy Technology Data Exchange (ETDEWEB)

Papadimitroulas, Panagiotis; Efthimiou, Nikos; Nikiforidis, George C.; Kagadis, George C. [Department of Medical Physics, School of Medicine, University of Patras, Rion, GR 265 04 (Greece); Loudos, George [Department of Biomedical Engineering, Technological Educational Institute of Athens, Ag. Spyridonos Street, Egaleo GR 122 10, Athens (Greece); Le Maitre, Amandine; Hatt, Mathieu; Tixier, Florent; Visvikis, Dimitris [Medical Information Processing Laboratory (LaTIM), National Institute of Health and Medical Research (INSERM), 29609 Brest (France)

2013-11-15

Purpose: The GATE Monte Carlo simulation toolkit is used for the implementation of realistic PET simulations incorporating tumor heterogeneous activity distributions. The reconstructed patient images include noise from the acquisition process, imaging system's performance restrictions and have limited spatial resolution. For those reasons, the measured intensity cannot be simply introduced in GATE simulations, to reproduce clinical data. Investigation of the heterogeneity distribution within tumors applying partial volume correction (PVC) algorithms was assessed. The purpose of the present study was to create a simulated oncology database based on clinical data with realistic intratumor uptake heterogeneity properties.Methods: PET/CT data of seven oncology patients were used in order to create a realistic tumor database investigating the heterogeneity activity distribution of the simulated tumors. The anthropomorphic models (NURBS based cardiac torso and Zubal phantoms) were adapted to the CT data of each patient, and the activity distribution was extracted from the respective PET data. The patient-specific models were simulated with the Monte Carlo Geant4 application for tomography emission (GATE) in three different levels for each case: (a) using homogeneous activity within the tumor, (b) using heterogeneous activity distribution in every voxel within the tumor as it was extracted from the PET image, and (c) using heterogeneous activity distribution corresponding to the clinical image following PVC. The three different types of simulated data in each case were reconstructed with two iterations and filtered with a 3D Gaussian postfilter, in order to simulate the intratumor heterogeneous uptake. Heterogeneity in all generated images was quantified using textural feature derived parameters in 3D according to the ground truth of the simulation, and compared to clinical measurements. Finally, profiles were plotted in central slices of the tumors, across lines

MOLECULAR DESCRIPTION OF ELECTROLYTE SOLUTION IN A CARBON AEROGEL ELECTRODE

Directory of Open Access Journals (Sweden)

A.Kovalenko

2003-01-01

Full Text Available We develop a molecular theory of aqueous electrolyte solution sorbed in a nanoporous carbon aerogel electrode, based on the replica reference interaction site model (replica RISM for realistic molecular quenched-annealed systems. We also briefly review applications of carbon aerogels for supercapacitor and electrochemical separation devices, as well as theoretical and computer modelling of disordered porous materials. The replica RISM integral equation theory yields the microscopic properties of the electrochemical double layer formed at the surface of carbon aerogel nanopores, with due account of chemical specificities of both sorbed electrolyte and carbon aerogel material. The theory allows for spatial disorder of aerogel pores in the range from micro- to macroscopic size scale. We considered ambient aqueous solution of 1 M sodium chloride sorbed in two model nanoporous carbon aerogels with carbon nanoparticles either arranged into branched chains or randomly distributed. The long-range correlations of the carbon aerogel nanostructure substantially affect the properties of the electrochemical double layer formed by the solution sorbed in nanopores.

Effects of classical and neo-classical cross-field transport of tungsten impurity in realistic tokamak geometry

Energy Technology Data Exchange (ETDEWEB)

Yamoto, S.; Inoue, H.; Sawada, Y.; Hatayama, A. [Faculty of Science and Technology, Keio University, Yokohama (Japan); Homma, Y.; Hoshino, K. [Japan Atomic Energy Agency, Rokkasho, Aomori (Japan); Bonnin, X. [ITER Organization, St. Paul Lez Durance (France); Coster, D. [Max-Planck-Institut fuer Plasmaphysik, Garching (Germany); Schneider, R. [Ernst-Moritz-Arndt University Greifswald (Germany)

2016-08-15

The initial simulation study of the neoclassical perpendicular self-diffusion transport in the SOL/Divertor regions for a realistic tokamak geometry with the IMPGYRO code has been performed in this paper. One of the most unique features of the IMPGYRO code is calculating exact Larmor orbit of the test particle instead of assuming guiding center approximation. Therefore, effects of the magnetic drifts in realistic tokamaks are naturally taken into account in the IMPGYRO code. This feature makes it possible to calculate neoclassical transport processes, which possibly become large in the SOL/divertor plasma. Indeed, neoclassical self-diffusion process, the resultant effect of the combination of magnetic drift and Coulomb collisions with background ions, has already been included in the IMPGYRO model. In the present paper, prior to implementing the detailed model of neoclassical transport process into IMPGYRO, we have investigated the effect of neoclassical selfdiffusion in a realistic tokamak geometry with lower single null X-point. We also use a model with guiding center approximation in order to compare with the IMPGYRO full orbit model. The preliminary calculation results of each model have shown differences in the perpendicular average velocity of impurity ions at the top region of the SOL. The mechanism which leads to the difference has been discussed. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Toward realistic pursuit-evasion using a roadmap-based approach

KAUST Repository

Rodriguez, Samuel; Denny, Jory; Burgos, Juan; Mahadevan, Aditya; Manavi, Kasra; Murray, Luke; Kodochygov, Anton; Zourntos, Takis; Amato, Nancy M.

2011-01-01

be applied to more realistic scenarios than are typically studied in most previous work, including agents moving in 3D environments such as terrains, multi-story buildings, and dynamic environments. We also support more realistic three-dimensional visibility

On Realistically Attacking Tor with Website Fingerprinting

Directory of Open Access Journals (Sweden)

Wang Tao

2016-10-01

Full Text Available Website fingerprinting allows a local, passive observer monitoring a web-browsing client’s encrypted channel to determine her web activity. Previous attacks have shown that website fingerprinting could be a threat to anonymity networks such as Tor under laboratory conditions. However, there are significant differences between laboratory conditions and realistic conditions. First, in laboratory tests we collect the training data set together with the testing data set, so the training data set is fresh, but an attacker may not be able to maintain a fresh data set. Second, laboratory packet sequences correspond to a single page each, but for realistic packet sequences the split between pages is not obvious. Third, packet sequences may include background noise from other types of web traffic. These differences adversely affect website fingerprinting under realistic conditions. In this paper, we tackle these three problems to bridge the gap between laboratory and realistic conditions for website fingerprinting. We show that we can maintain a fresh training set with minimal resources. We demonstrate several classification-based techniques that allow us to split full packet sequences effectively into sequences corresponding to a single page each. We describe several new algorithms for tackling background noise. With our techniques, we are able to build the first website fingerprinting system that can operate directly on packet sequences collected in the wild.

Normal and Pathological NCAT Image and PhantomData Based onPhysiologically Realistic Left Ventricle Finite-Element Models

Energy Technology Data Exchange (ETDEWEB)

Veress, Alexander I.; Segars, W. Paul; Weiss, Jeffrey A.; Tsui,Benjamin M.W.; Gullberg, Grant T.

2006-08-02

The 4D NURBS-based Cardiac-Torso (NCAT) phantom, whichprovides a realistic model of the normal human anatomy and cardiac andrespiratory motions, is used in medical imaging research to evaluate andimprove imaging devices and techniques, especially dynamic cardiacapplications. One limitation of the phantom is that it lacks the abilityto accurately simulate altered functions of the heart that result fromcardiac pathologies such as coronary artery disease (CAD). The goal ofthis work was to enhance the 4D NCAT phantom by incorporating aphysiologically based, finite-element (FE) mechanical model of the leftventricle (LV) to simulate both normal and abnormal cardiac motions. Thegeometry of the FE mechanical model was based on gated high-resolutionx-ray multi-slice computed tomography (MSCT) data of a healthy malesubject. The myocardial wall was represented as transversely isotropichyperelastic material, with the fiber angle varying from -90 degrees atthe epicardial surface, through 0 degreesat the mid-wall, to 90 degreesat the endocardial surface. A time varying elastance model was used tosimulate fiber contraction, and physiological intraventricular systolicpressure-time curves were applied to simulate the cardiac motion over theentire cardiac cycle. To demonstrate the ability of the FE mechanicalmodel to accurately simulate the normal cardiac motion as well abnormalmotions indicative of CAD, a normal case and two pathologic cases weresimulated and analyzed. In the first pathologic model, a subendocardialanterior ischemic region was defined. A second model was created with atransmural ischemic region defined in the same location. The FE baseddeformations were incorporated into the 4D NCAT cardiac model through thecontrol points that define the cardiac structures in the phantom whichwere set to move according to the predictions of the mechanical model. Asimulation study was performed using the FE-NCAT combination toinvestigate how the differences in contractile function

Iterated interactions method. Realistic NN potential

International Nuclear Information System (INIS)

Gorbatov, A.M.; Skopich, V.L.; Kolganova, E.A.

1991-01-01

The method of iterated potential is tested in the case of realistic fermionic systems. As a base for comparison calculations of the 16 O system (using various versions of realistic NN potentials) by means of the angular potential-function method as well as operators of pairing correlation were used. The convergence of genealogical series is studied for the central Malfliet-Tjon potential. In addition the mathematical technique of microscopical calculations is improved: new equations for correlators in odd states are suggested and the technique of leading terms was applied for the first time to calculations of heavy p-shell nuclei in the basis of angular potential functions

A novel model to assess the efficacy of steam surface pasteurization of cooked surimi gels inoculated with realistic levels of Listeria innocua.

Science.gov (United States)

Skåra, Torstein; Valdramidis, Vasilis P; Rosnes, Jan Thomas; Noriega, Estefanía; Van Impe, Jan F M

2014-12-01

Steam surface pasteurization is a promising decontamination technology for reducing pathogenic bacteria in different stages of food production. The effect of the artificial inoculation type and initial microbial load, however, has not been thoroughly assessed in the context of inactivation studies. In order to optimize the efficacy of the technology, the aim of this study was to design and validate a model system for steam surface pasteurization, assessing different inoculation methods and realistic microbial levels. More specifically, the response of Listeria innocua, a surrogate organism of Listeria monocytogenes, on a model fish product, and the effect of different inoculation levels following treatments with a steam surface pasteurization system was investigated. The variation in the resulting inoculation level on the samples was too large (77%) for the contact inoculation procedure to be further considered. In contrast, the variation of a drop inoculation procedure was 17%. Inoculation with high levels showed a rapid 1-2 log decrease after 3-5 s, and then no further inactivation beyond 20 s. A low level inoculation study was performed by analysing the treated samples using a novel contact plating approach, which can be performed without sample homogenization and dilution. Using logistic regression, results from this method were used to model the binary responses of Listeria on surfaces with realistic inoculation levels. According to this model, a treatment time of 23 s will result in a 1 log reduction (for P = 0.1). Copyright © 2014 Elsevier Ltd. All rights reserved.

Dynamics of leaf gas exchange, xylem and phloem transport, water potential and carbohydrate concentration in a realistic 3-D model tree crown.

Science.gov (United States)

Nikinmaa, Eero; Sievänen, Risto; Hölttä, Teemu

2014-09-01

Tree models simulate productivity using general gas exchange responses and structural relationships, but they rarely check whether leaf gas exchange and resulting water and assimilate transport and driving pressure gradients remain within acceptable physical boundaries. This study presents an implementation of the cohesion-tension theory of xylem transport and the Münch hypothesis of phloem transport in a realistic 3-D tree structure and assesses the gas exchange and transport dynamics. A mechanistic model of xylem and phloem transport was used, together with a tested leaf assimilation and transpiration model in a realistic tree architecture to simulate leaf gas exchange and water and carbohydrate transport within an 8-year-old Scots pine tree. The model solved the dynamics of the amounts of water and sucrose solute in the xylem, cambium and phloem using a fine-grained mesh with a system of coupled ordinary differential equations. The simulations predicted the observed patterns of pressure gradients and sugar concentration. Diurnal variation of environmental conditions influenced tree-level gradients in turgor pressure and sugar concentration, which are important drivers of carbon allocation. The results and between-shoot variation were sensitive to structural and functional parameters such as tree-level scaling of conduit size and phloem unloading. Linking whole-tree-level water and assimilate transport, gas exchange and sink activity opens a new avenue for plant studies, as features that are difficult to measure can be studied dynamically with the model. Tree-level responses to local and external conditions can be tested, thus making the approach described here a good test-bench for studies of whole-tree physiology.

Gradient models in molecular biophysics: progress, challenges, opportunities

Science.gov (United States)

Bardhan, Jaydeep P.

2013-12-01

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

A realistic multimodal modeling approach for the evaluation of distributed source analysis: application to sLORETA

Science.gov (United States)

Cosandier-Rimélé, D.; Ramantani, G.; Zentner, J.; Schulze-Bonhage, A.; Dümpelmann, M.

2017-10-01

Objective. Electrical source localization (ESL) deriving from scalp EEG and, in recent years, from intracranial EEG (iEEG), is an established method in epilepsy surgery workup. We aimed to validate the distributed ESL derived from scalp EEG and iEEG, particularly regarding the spatial extent of the source, using a realistic epileptic spike activity simulator. Approach. ESL was applied to the averaged scalp EEG and iEEG spikes of two patients with drug-resistant structural epilepsy. The ESL results for both patients were used to outline the location and extent of epileptic cortical patches, which served as the basis for designing a spatiotemporal source model. EEG signals for both modalities were then generated for different anatomic locations and spatial extents. ESL was subsequently performed on simulated signals with sLORETA, a commonly used distributed algorithm. ESL accuracy was quantitatively assessed for iEEG and scalp EEG. Main results. The source volume was overestimated by sLORETA at both EEG scales, with the error increasing with source size, particularly for iEEG. For larger sources, ESL accuracy drastically decreased, and reconstruction volumes shifted to the center of the head for iEEG, while remaining stable for scalp EEG. Overall, the mislocalization of the reconstructed source was more pronounced for iEEG. Significance. We present a novel multiscale framework for the evaluation of distributed ESL, based on realistic multiscale EEG simulations. Our findings support that reconstruction results for scalp EEG are often more accurate than for iEEG, owing to the superior 3D coverage of the head. Particularly the iEEG-derived reconstruction results for larger, widespread generators should be treated with caution.

A realistic multimodal modeling approach for the evaluation of distributed source analysis: application to sLORETA.

Science.gov (United States)

Cosandier-Rimélé, D; Ramantani, G; Zentner, J; Schulze-Bonhage, A; Dümpelmann, M

2017-10-01

Electrical source localization (ESL) deriving from scalp EEG and, in recent years, from intracranial EEG (iEEG), is an established method in epilepsy surgery workup. We aimed to validate the distributed ESL derived from scalp EEG and iEEG, particularly regarding the spatial extent of the source, using a realistic epileptic spike activity simulator. ESL was applied to the averaged scalp EEG and iEEG spikes of two patients with drug-resistant structural epilepsy. The ESL results for both patients were used to outline the location and extent of epileptic cortical patches, which served as the basis for designing a spatiotemporal source model. EEG signals for both modalities were then generated for different anatomic locations and spatial extents. ESL was subsequently performed on simulated signals with sLORETA, a commonly used distributed algorithm. ESL accuracy was quantitatively assessed for iEEG and scalp EEG. The source volume was overestimated by sLORETA at both EEG scales, with the error increasing with source size, particularly for iEEG. For larger sources, ESL accuracy drastically decreased, and reconstruction volumes shifted to the center of the head for iEEG, while remaining stable for scalp EEG. Overall, the mislocalization of the reconstructed source was more pronounced for iEEG. We present a novel multiscale framework for the evaluation of distributed ESL, based on realistic multiscale EEG simulations. Our findings support that reconstruction results for scalp EEG are often more accurate than for iEEG, owing to the superior 3D coverage of the head. Particularly the iEEG-derived reconstruction results for larger, widespread generators should be treated with caution.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

Science.gov (United States)

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis

2017-10-03

The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

KAUST Repository

Buin, Andrei; Comin, Riccardo; Ip, Alexander H.; Sargent, Edward H.

2015-01-01

© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

KAUST Repository

Buin, Andrei

2015-06-18

© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

Realistic modelling of external flooding scenarios - A multi-disciplinary approach

International Nuclear Information System (INIS)

Brinkman, J.L.

2014-01-01

against flooding and timing of the events into account as basis for the development and screening of flooding scenarios. Realistic modelling of external flooding scenarios in a PSA requires a multi-disciplinary approach. Next to being thoroughly familiar with the design features of the plant against flooding, like its critical elevations for safety (related) equipment and the strength of buildings, additional knowledge is necessary on design of flood protection measures as dikes and dunes, their failure behaviour and modelling. The approach does not change the basic flooding scenarios - the event tree structure - itself, but impacts the initiating event of the specific flooding scenarios. (authors)

Molecular Treatment of Nano-Kaolinite Generations.

Science.gov (United States)

Táborosi, Attila; Szilagyi, Robert K; Zsirka, Balázs; Fónagy, Orsolya; Horváth, Erzsébet; Kristóf, János

2018-06-18

A procedure is developed for defining a compositionally and structurally realistic, atomic-scale description of exfoliated clay nanoparticles from the kaolinite family of phylloaluminosilicates. By use of coordination chemical principles, chemical environments within a nanoparticle can be separated into inner, outer, and peripheral spheres. The edges of the molecular models of nanoparticles were protonated in a validated manner to achieve charge neutrality. Structural optimizations using semiempirical methods (NDDO Hamiltonians and DFTB formalism) and ab initio density functionals with a saturated basis set revealed previously overlooked molecular origins of morphological changes as a result of exfoliation. While the use of semiempirical methods is desirable for the treatment of nanoparticles composed of tens of thousands of atoms, the structural accuracy is rather modest in comparison to DFT methods. We report a comparative survey of our infrared data for untreated crystalline and various exfoliated states of kaolinite and halloysite. Given the limited availability of experimental techniques for providing direct structural information about nano-kaolinite, the vibrational spectra can be considered as an essential tool for validating structural models. The comparison of experimental and calculated stretching and bending frequencies further justified the use of the preferred level of theory. Overall, an optimal molecular model of the defect-free, ideal nano-kaolinite can be composed with respect to stationary structure and curvature of the potential energy surface using the PW91/SVP level of theory with empirical dispersion correction (PW91+D) and polarizable continuum solvation model (PCM) without the need for a scaled quantum chemical force field. This validated theoretical approach is essential in order to follow the formation of exfoliated clays and their surface reactivity that is experimentally unattainable.

Towards realistic molecular dynamics simulations of grain boundary mobility

International Nuclear Information System (INIS)

Zhou, J.; Mohles, V.

2011-01-01

In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21 o Σ7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.

The effect of problem posing and problem solving with realistic mathematics education approach to the conceptual understanding and adaptive reasoning

Science.gov (United States)

Mahendra, Rengga; Slamet, Isnandar; Budiyono

2017-12-01

One of the difficulties of students in learning mathematics is on the subject of geometry that requires students to understand abstract things. The aim of this research is to determine the effect of learning model Problem Posing and Problem Solving with Realistic Mathematics Education Approach to conceptual understanding and students' adaptive reasoning in learning mathematics. This research uses a kind of quasi experimental research. The population of this research is all seventh grade students of Junior High School 1 Jaten, Indonesia. The sample was taken using stratified cluster random sampling technique. The test of the research hypothesis was analyzed by using t-test. The results of this study indicate that the model of Problem Posing learning with Realistic Mathematics Education Approach can improve students' conceptual understanding significantly in mathematics learning. In addition tu, the results also showed that the model of Problem Solving learning with Realistic Mathematics Education Approach can improve students' adaptive reasoning significantly in learning mathematics. Therefore, the model of Problem Posing and Problem Solving learning with Realistic Mathematics Education Approach is appropriately applied in mathematics learning especially on the subject of geometry so as to improve conceptual understanding and students' adaptive reasoning. Furthermore, the impact can improve student achievement.

Two-Dimensional Model of Scrolled Packings of Molecular Nanoribbons

Science.gov (United States)

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

2018-04-01

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

Realistic multisite lattice-gas modeling and KMC simulation of catalytic surface reactions: Kinetics and multiscale spatial behavior for CO-oxidation on metal (1 0 0) surfaces

Science.gov (United States)

Liu, Da-Jiang; Evans, James W.

2013-12-01

A realistic molecular-level description of catalytic reactions on single-crystal metal surfaces can be provided by stochastic multisite lattice-gas (msLG) models. This approach has general applicability, although in this report, we will focus on the example of CO-oxidation on the unreconstructed fcc metal (1 0 0) or M(1 0 0) surfaces of common catalyst metals M = Pd, Rh, Pt and Ir (i.e., avoiding regimes where Pt and Ir reconstruct). These models can capture the thermodynamics and kinetics of adsorbed layers for the individual reactants species, such as CO/M(1 0 0) and O/M(1 0 0), as well as the interaction and reaction between different reactant species in mixed adlayers, such as (CO + O)/M(1 0 0). The msLG models allow population of any of hollow, bridge, and top sites. This enables a more flexible and realistic description of adsorption and adlayer ordering, as well as of reaction configurations and configuration-dependent barriers. Adspecies adsorption and interaction energies, as well as barriers for various processes, constitute key model input. The choice of these energies is guided by experimental observations, as well as by extensive Density Functional Theory analysis. Model behavior is assessed via Kinetic Monte Carlo (KMC) simulation. We also address the simulation challenges and theoretical ramifications associated with very rapid diffusion and local equilibration of reactant adspecies such as CO. These msLG models are applied to describe adsorption, ordering, and temperature programmed desorption (TPD) for individual CO/M(1 0 0) and O/M(1 0 0) reactant adlayers. In addition, they are also applied to predict mixed (CO + O)/M(1 0 0) adlayer structure on the nanoscale, the complete bifurcation diagram for reactive steady-states under continuous flow conditions, temperature programmed reaction (TPR) spectra, and titration reactions for the CO-oxidation reaction. Extensive and reasonably successful comparison of model predictions is made with experimental

Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

Science.gov (United States)

Aksela, Maija; Lundell, Jan

2008-01-01

Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…

Molecular models and simulations of layered materials

International Nuclear Information System (INIS)

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

2008-01-01

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

Modelling effects of diquat under realistic exposure patterns in genetically differentiated populations of the gastropod Lymnaea stagnalis.

Science.gov (United States)

Ducrot, Virginie; Péry, Alexandre R R; Lagadic, Laurent

2010-11-12

Pesticide use leads to complex exposure and response patterns in non-target aquatic species, so that the analysis of data from standard toxicity tests may result in unrealistic risk forecasts. Developing models that are able to capture such complexity from toxicity test data is thus a crucial issue for pesticide risk assessment. In this study, freshwater snails from two genetically differentiated populations of Lymnaea stagnalis were exposed to repeated acute applications of environmentally realistic concentrations of the herbicide diquat, from the embryo to the adult stage. Hatching rate, embryonic development duration, juvenile mortality, feeding rate and age at first spawning were investigated during both exposure and recovery periods. Effects of diquat on mortality were analysed using a threshold hazard model accounting for time-varying herbicide concentrations. All endpoints were significantly impaired at diquat environmental concentrations in both populations. Snail evolutionary history had no significant impact on their sensitivity and responsiveness to diquat, whereas food acted as a modulating factor of toxicant-induced mortality. The time course of effects was adequately described by the model, which thus appears suitable to analyse long-term effects of complex exposure patterns based upon full life cycle experiment data. Obtained model outputs (e.g. no-effect concentrations) could be directly used for chemical risk assessment.

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

Science.gov (United States)

Bardhan, Jaydeep P

2013-12-01

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

Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities

Science.gov (United States)

Bardhan, Jaydeep P.

2014-01-01

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

Normal and Pathological NCAT Image and Phantom Data Based on Physiologically Realistic Left Ventricle Finite-Element Models

International Nuclear Information System (INIS)

Veress, Alexander I.; Segars, W. Paul; Weiss, Jeffrey A.; Tsui, Benjamin M.W.; Gullberg, Grant T.

2006-01-01

The 4D NURBS-based Cardiac-Torso (NCAT) phantom, which provides a realistic model of the normal human anatomy and cardiac and respiratory motions, is used in medical imaging research to evaluate and improve imaging devices and techniques, especially dynamic cardiac applications. One limitation of the phantom is that it lacks the ability to accurately simulate altered functions of the heart that result from cardiac pathologies such as coronary artery disease (CAD). The goal of this work was to enhance the 4D NCAT phantom by incorporating a physiologically based, finite-element (FE) mechanical model of the left ventricle (LV) to simulate both normal and abnormal cardiac motions. The geometry of the FE mechanical model was based on gated high-resolution x-ray multi-slice computed tomography (MSCT) data of a healthy male subject. The myocardial wall was represented as transversely isotropichyperelastic material, with the fiber angle varying from -90 degrees at the epicardial surface, through 0 degrees at the mid-wall, to 90 degrees at the endocardial surface. A time varying elastance model was used to simulate fiber contraction, and physiological intraventricular systolic pressure-time curves were applied to simulate the cardiac motion over the entire cardiac cycle. To demonstrate the ability of the FE mechanical model to accurately simulate the normal cardiac motion as well abnormal motions indicative of CAD, a normal case and two pathologic cases were simulated and analyzed. In the first pathologic model, a subendocardial anterior ischemic region was defined. A second model was created with a transmural ischemic region defined in the same location. The FE based deformations were incorporated into the 4D NCAT cardiac model through the control points that define the cardiac structures in the phantom which were set to move according to the predictions of the mechanical model. A simulation study was performed using the FE-NCAT combination to investigate how the

Dynamic apeerture in damping rings with realistic wigglers

Energy Technology Data Exchange (ETDEWEB)

Cai, Yunhai; /SLAC

2005-05-04

The International Linear Collider based on superconducting RF cavities requires the damping rings to have extremely small equilibrium emittance, huge circumference, fast damping time, and large acceptance. To achieve all of these requirements is a very challenging task. In this paper, we will present a systematic approach to designing the damping rings using simple cells and non-interlaced sextupoles. The designs of the damping rings with various circumferences and shapes, including dogbone, are presented. To model realistic wigglers, we have developed a new hybrid symplectic integrator for faster and accurate evaluation of dynamic aperture of the lattices.

A Novel CPU/GPU Simulation Environment for Large-Scale Biologically-Realistic Neural Modeling

Directory of Open Access Journals (Sweden)

Roger V Hoang

2013-10-01

Full Text Available Computational Neuroscience is an emerging field that provides unique opportunities to studycomplex brain structures through realistic neural simulations. However, as biological details are added tomodels, the execution time for the simulation becomes longer. Graphics Processing Units (GPUs are now being utilized to accelerate simulations due to their ability to perform computations in parallel. As such, they haveshown significant improvement in execution time compared to Central Processing Units (CPUs. Most neural simulators utilize either multiple CPUs or a single GPU for better performance, but still show limitations in execution time when biological details are not sacrificed. Therefore, we present a novel CPU/GPU simulation environment for large-scale biological networks,the NeoCortical Simulator version 6 (NCS6. NCS6 is a free, open-source, parallelizable, and scalable simula-tor, designed to run on clusters of multiple machines, potentially with high performance computing devicesin each of them. It has built-in leaky-integrate-and-fire (LIF and Izhikevich (IZH neuron models, but usersalso have the capability to design their own plug-in interface for different neuron types as desired. NCS6is currently able to simulate one million cells and 100 million synapses in quasi real time by distributing dataacross these heterogeneous clusters of CPUs and GPUs.

A Low-cost System for Generating Near-realistic Virtual Actors

Science.gov (United States)

Afifi, Mahmoud; Hussain, Khaled F.; Ibrahim, Hosny M.; Omar, Nagwa M.

2015-06-01

Generating virtual actors is one of the most challenging fields in computer graphics. The reconstruction of a realistic virtual actor has been paid attention by the academic research and the film industry to generate human-like virtual actors. Many movies were acted by human-like virtual actors, where the audience cannot distinguish between real and virtual actors. The synthesis of realistic virtual actors is considered a complex process. Many techniques are used to generate a realistic virtual actor; however they usually require expensive hardware equipment. In this paper, a low-cost system that generates near-realistic virtual actors is presented. The facial features of the real actor are blended with a virtual head that is attached to the actor's body. Comparing with other techniques that generate virtual actors, the proposed system is considered a low-cost system that requires only one camera that records the scene without using any expensive hardware equipment. The results of our system show that the system generates good near-realistic virtual actors that can be used on many applications.

Mathematics Instructional Model Based on Realistic Mathematics Education to Promote Problem Solving Ability at Junior High School Padang

Directory of Open Access Journals (Sweden)

Edwin Musdi

2016-02-01

Full Text Available This research aims to develop a mathematics instructional model based realistic mathematics education (RME to promote students' problem-solving abilities. The design research used Plomp models, which consists of preliminary phase, development or proto-typing phase and assessment phase.  At this study, only the first two phases conducted. The first phase, a preliminary investigation, carried out with a literature study to examine the theory-based instructional learning RME model, characteristics of learners, learning management descriptions by junior high school mathematics teacher and relevant research. The development phase is done by developing a draft model (an early prototype model that consists of the syntax, the social system, the principle of reaction, support systems, and the impact and effects of instructional support. Early prototype model contain a draft model, lesson plans, worksheets, and assessments. Tesssmer formative evaluation model used to revise the model. In this study only phase of one to one evaluation conducted. In the ppreliminary phase has produced a theory-based learning RME model, a description of the characteristics of learners in grade VIII Junior High School Padang and the description of teacher teaching in the classroom. The result showed that most students were still not be able to solve the non-routine problem. Teachers did not optimally facilitate students to develop problem-solving skills of students. It was recommended that the model can be applied in the classroom.

Convective aggregation in realistic convective-scale simulations

Science.gov (United States)

Holloway, Christopher E.

2017-06-01

To investigate the real-world relevance of idealized-model convective self-aggregation, five 15 day cases of real organized convection in the tropics are simulated. These include multiple simulations of each case to test sensitivities of the convective organization and mean states to interactive radiation, interactive surface fluxes, and evaporation of rain. These simulations are compared to self-aggregation seen in the same model configured to run in idealized radiative-convective equilibrium. Analysis of the budget of the spatial variance of column-integrated frozen moist static energy shows that control runs have significant positive contributions to organization from radiation and negative contributions from surface fluxes and transport, similar to idealized runs once they become aggregated. Despite identical lateral boundary conditions for all experiments in each case, systematic differences in mean column water vapor (CWV), CWV distribution shape, and CWV autocorrelation length scale are found between the different sensitivity runs, particularly for those without interactive radiation, showing that there are at least some similarities in sensitivities to these feedbacks in both idealized and realistic simulations (although the organization of precipitation shows less sensitivity to interactive radiation). The magnitudes and signs of these systematic differences are consistent with a rough equilibrium between (1) equalization due to advection from the lateral boundaries and (2) disaggregation due to the absence of interactive radiation, implying disaggregation rates comparable to those in idealized runs with aggregated initial conditions and noninteractive radiation. This points to a plausible similarity in the way that radiation feedbacks maintain aggregated convection in both idealized simulations and the real world.Plain Language SummaryUnderstanding the processes that lead to the organization of tropical rainstorms is an important challenge for weather

Modeling molecular boiling points using computed interaction energies.

Science.gov (United States)

Peterangelo, Stephen C; Seybold, Paul G

2017-12-20

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

Designing field-controllable graphene-dot-graphene single molecule switches: A quantum-theoretical proof-of-concept under realistic operating conditions.

Science.gov (United States)

Pejov, Ljupčo; Petreska, Irina; Kocarev, Ljupčo

2015-12-28

A theoretical proof of the concept that a particularly designed graphene-based moletronics device, constituted by two semi-infinite graphene subunits, acting as source and drain electrodes, and a central benzenoid ring rotator (a "quantum dot"), could act as a field-controllable molecular switch is outlined and analyzed with the density functional theory approach. Besides the ideal (0 K) case, we also consider the operation of such a device under realistic operating (i.e., finite-temperature) conditions. An in-depth insight into the physics behind device controllability by an external field was gained by thorough analyses of the torsional potential of the dot under various conditions (absence or presence of an external gating field with varying strength), computing the torsional correlation time and transition probabilities within the Bloembergen-Purcell-Pound formalism. Both classical and quantum mechanical tunneling contributions to the intramolecular rotation were considered in the model. The main idea that we put forward in the present study is that intramolecular rotors can be controlled by the gating field even in cases when these groups do not possess a permanent dipole moment (as in cases considered previously by us [I. Petreska et al., J. Chem. Phys. 134, 014708-1-014708-12 (2011)] and also by other groups [P. E. Kornilovitch et al., Phys. Rev. B 66, 245413-1-245413-7 (2002)]). Consequently, one can control the molecular switching properties by an external electrostatic field utilizing even nonpolar intramolecular rotors (i.e., in a more general case than those considered so far). Molecular admittance of the currently considered graphene-based molecular switch under various conditions is analyzed employing non-equilibrium Green's function formalism, as well as by analysis of frontier molecular orbitals' behavior.

Progress in realistic LOCA analysis

Energy Technology Data Exchange (ETDEWEB)

Young, M Y; Bajorek, S M; Ohkawa, K [Westinghouse Electric Corporation, Pittsburgh, PA (United States)

1994-12-31

While LOCA is a complex transient to simulate, the state of art in thermal hydraulics has advanced sufficiently to allow its realistic prediction and application of advanced methods to actual reactor design as demonstrated by methodology described in this paper 6 refs, 5 figs, 3 tabs

Should scientific realists be platonists?

DEFF Research Database (Denmark)

Busch, Jacob; Morrison, Joe

2015-01-01

an appropriate use of the resources of Scientific Realism (in particular, IBE) to achieve platonism? (§2) We argue that just because a variety of different inferential strategies can be employed by Scientific Realists does not mean that ontological conclusions concerning which things we should be Scientific...

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

Science.gov (United States)

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

A Data-Driven Approach to Realistic Shape Morphing

KAUST Repository

Gao, Lin; Lai, Yu-Kun; Huang, Qi-Xing; Hu, Shi-Min

2013-01-01

Morphing between 3D objects is a fundamental technique in computer graphics. Traditional methods of shape morphing focus on establishing meaningful correspondences and finding smooth interpolation between shapes. Such methods however only take geometric information as input and thus cannot in general avoid producing unnatural interpolation, in particular for large-scale deformations. This paper proposes a novel data-driven approach for shape morphing. Given a database with various models belonging to the same category, we treat them as data samples in the plausible deformation space. These models are then clustered to form local shape spaces of plausible deformations. We use a simple metric to reasonably represent the closeness between pairs of models. Given source and target models, the morphing problem is casted as a global optimization problem of finding a minimal distance path within the local shape spaces connecting these models. Under the guidance of intermediate models in the path, an extended as-rigid-as-possible interpolation is used to produce the final morphing. By exploiting the knowledge of plausible models, our approach produces realistic morphing for challenging cases as demonstrated by various examples in the paper. © 2013 The Eurographics Association and Blackwell Publishing Ltd.

A Data-Driven Approach to Realistic Shape Morphing

KAUST Repository

Gao, Lin

2013-05-01

Morphing between 3D objects is a fundamental technique in computer graphics. Traditional methods of shape morphing focus on establishing meaningful correspondences and finding smooth interpolation between shapes. Such methods however only take geometric information as input and thus cannot in general avoid producing unnatural interpolation, in particular for large-scale deformations. This paper proposes a novel data-driven approach for shape morphing. Given a database with various models belonging to the same category, we treat them as data samples in the plausible deformation space. These models are then clustered to form local shape spaces of plausible deformations. We use a simple metric to reasonably represent the closeness between pairs of models. Given source and target models, the morphing problem is casted as a global optimization problem of finding a minimal distance path within the local shape spaces connecting these models. Under the guidance of intermediate models in the path, an extended as-rigid-as-possible interpolation is used to produce the final morphing. By exploiting the knowledge of plausible models, our approach produces realistic morphing for challenging cases as demonstrated by various examples in the paper. © 2013 The Eurographics Association and Blackwell Publishing Ltd.

Scaling up complex interventions: insights from a realist synthesis.

Science.gov (United States)

Willis, Cameron D; Riley, Barbara L; Stockton, Lisa; Abramowicz, Aneta; Zummach, Dana; Wong, Geoff; Robinson, Kerry L; Best, Allan

2016-12-19

Preventing chronic diseases, such as cancer, cardiovascular disease and diabetes, requires complex interventions, involving multi-component and multi-level efforts that are tailored to the contexts in which they are delivered. Despite an increasing number of complex interventions in public health, many fail to be 'scaled up'. This study aimed to increase understanding of how and under what conditions complex public health interventions may be scaled up to benefit more people and populations.A realist synthesis was conducted and discussed at an in-person workshop involving practitioners responsible for scaling up activities. Realist approaches view causality through the linkages between changes in contexts (C) that activate mechanisms (M), leading to specific outcomes (O) (CMO configurations). To focus this review, three cases of complex interventions that had been successfully scaled up were included: Vibrant Communities, Youth Build USA and Pathways to Education. A search strategy of published and grey literature related to each case was developed, involving searches of relevant databases and nominations from experts. Data extracted from included documents were classified according to CMO configurations within strategic themes. Findings were compared and contrasted with guidance from diffusion theory, and interpreted with knowledge users to identify practical implications and potential directions for future research.Four core mechanisms were identified, namely awareness, commitment, confidence and trust. These mechanisms were activated within two broad scaling up strategies, those of renewing and regenerating, and documenting success. Within each strategy, specific actions to change contexts included building partnerships, conducting evaluations, engaging political support and adapting funding models. These modified contexts triggered the identified mechanisms, leading to a range of scaling up outcomes, such as commitment of new communities, changes in relevant

Viscoelasticity in Polymers: Phenomenological to Molecular Mathematical Modelling

National Research Council Canada - National Science Library

Banks, H. T; Luke, N. S

2006-01-01

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

Molecular modeling of protein materials: case study of elastin

International Nuclear Information System (INIS)

Tarakanova, Anna; Buehler, Markus J

2013-01-01

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

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

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

2009-01-01

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

Time management: a realistic approach.

Science.gov (United States)

Jackson, Valerie P

2009-06-01

Realistic time management and organization plans can improve productivity and the quality of life. However, these skills can be difficult to develop and maintain. The key elements of time management are goals, organization, delegation, and relaxation. The author addresses each of these components and provides suggestions for successful time management.

What works for whom in pharmacist-led smoking cessation support: realist review.

Science.gov (United States)

Greenhalgh, Trisha; Macfarlane, Fraser; Steed, Liz; Walton, Robert

2016-12-16

New models of primary care are needed to address funding and staffing pressures. We addressed the research question "what works for whom in what circumstances in relation to the role of community pharmacies in providing lifestyle interventions to support smoking cessation?" This is a realist review conducted according to RAMESES standards. We began with a sample of 103 papers included in a quantitative review of community pharmacy intervention trials identified through systematic searching of seven databases. We supplemented this with additional papers: studies that had been excluded from the quantitative review but which provided rigorous and relevant additional data for realist theorising; citation chaining (pursuing reference lists and Google Scholar forward tracking of key papers); the 'search similar citations' function on PubMed. After mapping what research questions had been addressed by these studies and how, we undertook a realist analysis to identify and refine candidate theories about context-mechanism-outcome configurations. Our final sample consisted of 66 papers describing 74 studies (12 systematic reviews, 6 narrative reviews, 18 RCTs, 1 process detail of a RCT, 1 cost-effectiveness study, 12 evaluations of training, 10 surveys, 8 qualitative studies, 2 case studies, 2 business models, 1 development of complex intervention). Most studies had been undertaken in the field of pharmacy practice (pharmacists studying what pharmacists do) and demonstrated the success of pharmacist training in improving confidence, knowledge and (in many but not all studies) patient outcomes. Whilst a few empirical studies had applied psychological theories to account for behaviour change in pharmacists or people attempting to quit, we found no studies that had either developed or tested specific theoretical models to explore how pharmacists' behaviour may be affected by organisational context. Because of the nature of the empirical data, only a provisional realist analysis

How realistic are air quality hindcasts driven by forcings from climate model simulations?

Science.gov (United States)

Lacressonnière, G.; Peuch, V.-H.; Arteta, J.; Josse, B.; Joly, M.; Marécal, V.; Saint Martin, D.; Déqué, M.; Watson, L.

2012-12-01

Predicting how European air quality could evolve over the next decades in the context of changing climate requires the use of climate models to produce results that can be averaged in a climatologically and statistically sound manner. This is a very different approach from the one that is generally used for air quality hindcasts for the present period; analysed meteorological fields are used to represent specifically each date and hour. Differences arise both from the fact that a climate model run results in a pure model output, with no influence from observations (which are useful to correct for a range of errors), and that in a "climate" set-up, simulations on a given day, month or even season cannot be related to any specific period of time (but can just be interpreted in a climatological sense). Hence, although an air quality model can be thoroughly validated in a "realistic" set-up using analysed meteorological fields, the question remains of how far its outputs can be interpreted in a "climate" set-up. For this purpose, we focus on Europe and on the current decade using three 5-yr simulations performed with the multiscale chemistry-transport model MOCAGE and use meteorological forcings either from operational meteorological analyses or from climate simulations. We investigate how statistical skill indicators compare in the different simulations, discriminating also the effects of meteorology on atmospheric fields (winds, temperature, humidity, pressure, etc.) and on the dependent emissions and deposition processes (volatile organic compound emissions, deposition velocities, etc.). Our results show in particular how differing boundary layer heights and deposition velocities affect horizontal and vertical distributions of species. When the model is driven by operational analyses, the simulation accurately reproduces the observed values of O3, NOx, SO2 and, with some bias that can be explained by the set-up, PM10. We study how the simulations driven by climate

A realistic intersecting D6-brane model after the first LHC run

Science.gov (United States)

Li, Tianjun; Nanopoulos, D. V.; Raza, Shabbar; Wang, Xiao-Chuan

2014-08-01

With the Higgs boson mass around 125 GeV and the LHC supersymmetry search constraints, we revisit a three-family Pati-Salam model from intersecting D6-branes in Type IIA string theory on the T 6/(ℤ2 × ℤ2) orientifold which has a realistic phenomenology. We systematically scan the parameter space for μ 0, and find that the gravitino mass is generically heavier than about 2 TeV for both cases due to the Higgs mass low bound 123 GeV. In particular, we identify a region of parameter space with the electroweak fine-tuning as small as Δ EW ~ 24-32 (3-4%). In the viable parameter space which is consistent with all the current constraints, the mass ranges for gluino, the first two-generation squarks and sleptons are respectively [3, 18] TeV, [3, 16] TeV, and [2, 7] TeV. For the third-generation sfermions, the light stop satisfying 5 σ WMAP bounds via neutralino-stop coannihilation has mass from 0.5 to 1.2 TeV, and the light stau can be as light as 800 GeV. We also show various coannihilation and resonance scenarios through which the observed dark matter relic density is achieved. Interestingly, the certain portions of parameter space has excellent t- b- τ and b- τ Yukawa coupling unification. Three regions of parameter space are highlighted as well where the dominant component of the lightest neutralino is a bino, wino or higgsino. We discuss various scenarios in which such solutions may avoid recent astrophysical bounds in case if they satisfy or above observed relic density bounds. Prospects of finding higgsino-like neutralino in direct and indirect searches are also studied. And we display six tables of benchmark points depicting various interesting features of our model. Note that the lightest neutralino can be heavy up to 2.8 TeV, and there exists a natural region of parameter space from low-energy fine-tuning definition with heavy gluino and first two-generation squarks/sleptons, we point out that the 33 TeV and 100 TeV proton-proton colliders are indeed

Modelling the performance of interferometric gravitational-wave detectors with realistically imperfect optics

Science.gov (United States)

Bochner, Brett

1998-12-01

The LIGO project is part of a world-wide effort to detect the influx of Gravitational Waves upon the earth from astrophysical sources, via their interaction with laser beams in interferometric detectors that are designed for extraordinarily high sensitivity. Central to the successful performance of LIGO detectors is the quality of their optical components, and the efficient optimization of interferometer configuration parameters. To predict LIGO performance with optics possessing realistic imperfections, we have developed a numerical simulation program to compute the steady-state electric fields of a complete, coupled-cavity LIGO interferometer. The program can model a wide variety of deformations, including laser beam mismatch and/or misalignment, finite mirror size, mirror tilts, curvature distortions, mirror surface roughness, and substrate inhomogeneities. Important interferometer parameters are automatically optimized during program execution to achieve the best possible sensitivity for each new set of perturbed mirrors. This thesis includes investigations of two interferometer designs: the initial LIGO system, and an advanced LIGO configuration called Dual Recycling. For Initial-LIGO simulations, the program models carrier and sideband frequency beams to compute the explicit shot-noise-limited gravitational wave sensitivity of the interferometer. It is demonstrated that optics of exceptional quality (root-mean-square deformations of less than ~1 nm in the central mirror regions) are necessary to meet Initial-LIGO performance requirements, but that they can be feasibly met. It is also shown that improvements in mirror quality can substantially increase LIGO's sensitivity to selected astrophysical sources. For Dual Recycling, the program models gravitational- wave-induced sidebands over a range of frequencies to demonstrate that the tuned and narrow-banded signal responses predicted for this configuration can be achieved with imperfect optics. Dual Recycling

Development of realistic high-resolution whole-body voxel models of Japanese adult males and females of average height and weight, and application of models to radio-frequency electromagnetic-field dosimetry

International Nuclear Information System (INIS)

Nagaoka, Tomoaki; Watanabe, Soichi; Sakurai, Kiyoko; Kunieda, Etsuo; Watanabe, Satoshi; Taki, Masao; Yamanaka, Yukio

2004-01-01

With advances in computer performance, the use of high-resolution voxel models of the entire human body has become more frequent in numerical dosimetries of electromagnetic waves. Using magnetic resonance imaging, we have developed realistic high-resolution whole-body voxel models for Japanese adult males and females of average height and weight. The developed models consist of cubic voxels of 2 mm on each side; the models are segmented into 51 anatomic regions. The adult female model is the first of its kind in the world and both are the first Asian voxel models (representing average Japanese) that enable numerical evaluation of electromagnetic dosimetry at high frequencies of up to 3 GHz. In this paper, we will also describe the basic SAR characteristics of the developed models for the VHF/UHF bands, calculated using the finite-difference time-domain method

A linear evolution for non-linear dynamics and correlations in realistic nuclei

International Nuclear Information System (INIS)

Levin, E.; Lublinsky, M.

2004-01-01

A new approach to high energy evolution based on a linear equation for QCD generating functional is developed. This approach opens a possibility for systematic study of correlations inside targets, and, in particular, inside realistic nuclei. Our results are presented as three new equations. The first one is a linear equation for QCD generating functional (and for scattering amplitude) that sums the 'fan' diagrams. For the amplitude this equation is equivalent to the non-linear Balitsky-Kovchegov equation. The second equation is a generalization of the Balitsky-Kovchegov non-linear equation to interactions with realistic nuclei. It includes a new correlation parameter which incorporates, in a model-dependent way, correlations inside the nuclei. The third equation is a non-linear equation for QCD generating functional (and for scattering amplitude) that in addition to the 'fan' diagrams sums the Glauber-Mueller multiple rescatterings

Population of 224 realistic human subject-based computational breast phantoms

Energy Technology Data Exchange (ETDEWEB)

Erickson, David W. [Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States); Wells, Jered R., E-mail: jered.wells@duke.edu [Clinical Imaging Physics Group and Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States); Sturgeon, Gregory M. [Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 (United States); Samei, Ehsan [Department of Radiology and Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Departments of Physics, Electrical and Computer Engineering, and Biomedical Engineering, and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States); Dobbins, James T. [Department of Radiology and Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Departments of Physics and Biomedical Engineering and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States); Segars, W. Paul [Department of Radiology and Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States); Lo, Joseph Y. [Department of Radiology and Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705 and Departments of Electrical and Computer Engineering and Biomedical Engineering and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27705 (United States)

2016-01-15

Purpose: To create a database of highly realistic and anatomically variable 3D virtual breast phantoms based on dedicated breast computed tomography (bCT) data. Methods: A tissue classification and segmentation algorithm was used to create realistic and detailed 3D computational breast phantoms based on 230 + dedicated bCT datasets from normal human subjects. The breast volume was identified using a coarse three-class fuzzy C-means segmentation algorithm which accounted for and removed motion blur at the breast periphery. Noise in the bCT data was reduced through application of a postreconstruction 3D bilateral filter. A 3D adipose nonuniformity (bias field) correction was then applied followed by glandular segmentation using a 3D bias-corrected fuzzy C-means algorithm. Multiple tissue classes were defined including skin, adipose, and several fractional glandular densities. Following segmentation, a skin mask was produced which preserved the interdigitated skin, adipose, and glandular boundaries of the skin interior. Finally, surface modeling was used to produce digital phantoms with methods complementary to the XCAT suite of digital human phantoms. Results: After rejecting some datasets due to artifacts, 224 virtual breast phantoms were created which emulate the complex breast parenchyma of actual human subjects. The volume breast density (with skin) ranged from 5.5% to 66.3% with a mean value of 25.3% ± 13.2%. Breast volumes ranged from 25.0 to 2099.6 ml with a mean value of 716.3 ± 386.5 ml. Three breast phantoms were selected for imaging with digital compression (using finite element modeling) and simple ray-tracing, and the results show promise in their potential to produce realistic simulated mammograms. Conclusions: This work provides a new population of 224 breast phantoms based on in vivo bCT data for imaging research. Compared to previous studies based on only a few prototype cases, this dataset provides a rich source of new cases spanning a wide range

Realistic nuclear shell theory and the doubly-magic 132Sn region

International Nuclear Information System (INIS)

Vary, J.P.

1978-01-01

After an introduction discussing the motivation and interest in results obtained with isotope separators, the fundamental problem in realistic nuclear shell theory is posed in the context of renormalization theory. Then some of the important developments that have occurred over the last fifteen years in the derivation of the effective Hamiltonian and application of realistic nuclear shell theory are briefly reviewed. Doubly magic regions of the periodic table and the unique advantages of the 132 Sn region are described. Then results are shown for the ground-state properties of 132 Sn as calculated from the density-dependent Hartree-Fock approach with the Skyrme Hamiltonian. A single theoretical Hamiltonian for all nuclei from doubly magic 132 Sn to doubly magic 208 Pb is presented; single-particle energies are graphed. Finally, predictions of shell-model level-density distributions obtained with spectral distribution methods are discussed; calculated level densities are shown for 136 Xe. 10 figures

Molecular modeling in confined polymer and biomembrane systems

Directory of Open Access Journals (Sweden)

Jayeeta Ghosh

2009-07-01

Full Text Available The computational study of soft materials under confinement for bio- and nanotechnology still poses significantchallenges but has come a long way in the last decade. It is possible to realistically model and understand the fundamentalmechanisms which are at play if soft materials are confined to nanometer dimensions. Here, we present several recentexamples of such studies. Thin polymer films are abundantly used as friction modifiers or steric stabilizers. We show howsystematic modeling can shed light on the interplay between entropic and energetic interactions. Thin glassy films arecritical for the success of nanolithography. For that we have to understand the effect of confinement on the glass transitionbehavior in order to guarantee the stability and integrity of the lithographic masks. Simulations aim to understand the fundamental differences in the densities of states of glass formers in bulk and under confinement. With the advent of bionanotechnology the structure and phase behavior of lipid membranes as models for cellular membranes at the nano scale length is of importance due to implications in understanding the role of the lipids in biochemical membrane processes.

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.

Theoretical model for calculation of molecular stopping power

International Nuclear Information System (INIS)

Xu, Y.J.

1984-01-01

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

Spherical convolutions and their application in molecular modelling

DEFF Research Database (Denmark)

Boomsma, Wouter; Frellsen, Jes

2017-01-01

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

Realistic methods for calculating the releases and consequences of a large LOCA

International Nuclear Information System (INIS)

Stephenson, W.; Dutton, L.M.C.; Handy, B.J.; Smedley, C.

1992-01-01

This report describes a calculational route to predict realistic radiological consequences for a successfully terminated large-loss-of-coolant accident (LOCA) at a pressurized-water reactor (PWR). All steps in the calculational route are considered. For each one, a brief comment is made on the significant differences between the methods of calculation that were identified in the benchmark studies and recommendations are made for the methods and data for carrying out realistic calculations. These are based on the best supportable methods and data and the technical basis for each recommendation is given. Where the lack of well-validated methods or data means that the most realistic method that can be justified is considered to be very conservative, the need for further research is identified. The behaviour of inorganic iodine and the removal of aerosols from the atmosphere of the reactor building are identified as areas of particular importance. Where the retention of radioactivity is sensitive to design features, these are identified and, for the most importance features, the impact of different designs on the release of activity is indicated. The predictions of the proposed model are calculated for each stage and compared with the releases of activity predicted by the licensing methods that were used in the earlier benchmark studies. The conservative nature of the latter is confirmed. Methods and data are also presented for calculating the resulting doses to members of the public of the National Radiological Protection Boards as a result of work carried out by several national bodies in the UK. Other, equally acceptable, models are used in other countries of the Community and some examples are given

Supernova Driving. IV. The star-formation rate of molecular clouds

DEFF Research Database (Denmark)

Padoan, Paolo; Haugbølle, Troels; Nordlund, Åke

2017-01-01

We compute the star-formation rate (SFR) in molecular clouds (MCs) that originate ab initio in a new, higher-resolution simulation of supernova-driven turbulence. Because of the large number of well-resolved clouds with self-consistent boundary and initial conditions, we obtain a large range...... of cloud physical parameters with realistic statistical distributions, which is an unprecedented sample of star-forming regions to test SFR models and to interpret observational surveys. We confirm the dependence of the SFR per free-fall time, SFRff, on the virial parameter, αvir, found in previous...... MCs and in clouds near the Galactic center. Although not explicitly modeled by the theory, the scatter is consistent with the physical assumptions of our revised model and may also result in part from a lack of statistical equilibrium of the turbulence, due to the transient nature of MCs....

Simulation of microarray data with realistic characteristics

Directory of Open Access Journals (Sweden)

Lehmussola Antti

2006-07-01

Full Text Available Abstract Background Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed for analyzing the data. However, an objective evaluation of the proposed algorithms is not possible due to the lack of biological ground truth information. To overcome this fundamental problem, the use of simulated microarray data for algorithm validation has been proposed. Results We present a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics. The applicability of the proposed model is demonstrated by several examples. Conclusion The proposed microarray simulation model is modular and can be used in different kinds of applications. It includes several error models that have been proposed earlier and it can be used with different types of input data. The model can be used to simulate both spotted two-channel and oligonucleotide based single-channel microarrays. All this makes the model a valuable tool for example in validation of data analysis algorithms.

Realistic Scheduling Mechanism for Smart Homes

Directory of Open Access Journals (Sweden)

Danish Mahmood

2016-03-01

Full Text Available In this work, we propose a Realistic Scheduling Mechanism (RSM to reduce user frustration and enhance appliance utility by classifying appliances with respective constraints and their time of use effectively. Algorithms are proposed regarding functioning of home appliances. A 24 hour time slot is divided into four logical sub-time slots, each composed of 360 min or 6 h. In these sub-time slots, only desired appliances (with respect to appliance classification are scheduled to raise appliance utility, restricting power consumption by a dynamically modelled power usage limiter that does not only take the electricity consumer into account but also the electricity supplier. Once appliance, time and power usage limiter modelling is done, we use a nature-inspired heuristic algorithm, Binary Particle Swarm Optimization (BPSO, optimally to form schedules with given constraints representing each sub-time slot. These schedules tend to achieve an equilibrium amongst appliance utility and cost effectiveness. For validation of the proposed RSM, we provide a comparative analysis amongst unscheduled electrical load usage, scheduled directly by BPSO and RSM, reflecting user comfort, which is based upon cost effectiveness and appliance utility.

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

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

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

Observational Constraints for Modeling Diffuse Molecular Clouds

Science.gov (United States)

Federman, S. R.

2014-02-01

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

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...

A realistic closed-form radiobiological model of clinical tumor-control data incorporating intertumor heterogeneity

International Nuclear Information System (INIS)

Roberts, Stephen A.; Hendry, Jolyon H.

1998-01-01

Purpose: To investigate the role of intertumor heterogeneity in clinical tumor control datasets and the relationship to in vitro measurements of tumor biopsy samples. Specifically, to develop a modified linear-quadratic (LQ) model incorporating such heterogeneity that it is practical to fit to clinical tumor-control datasets. Methods and Materials: We developed a modified version of the linear-quadratic (LQ) model for tumor control, incorporating a (lagged) time factor to allow for tumor cell repopulation. We explicitly took into account the interpatient heterogeneity in clonogen number, radiosensitivity, and repopulation rate. Using this model, we could generate realistic TCP curves using parameter estimates consistent with those reported from in vitro studies, subject to the inclusion of a radiosensitivity (or dose)-modifying factor. We then demonstrated that the model was dominated by the heterogeneity in α (tumor radiosensitivity) and derived an approximate simplified model incorporating this heterogeneity. This simplified model is expressible in a compact closed form, which it is practical to fit to clinical datasets. Using two previously analysed datasets, we fit the model using direct maximum-likelihood techniques and obtained parameter estimates that were, again, consistent with the experimental data on the radiosensitivity of primary human tumor cells. This heterogeneity model includes the same number of adjustable parameters as the standard LQ model. Results: The modified model provides parameter estimates that can easily be reconciled with the in vitro measurements. The simplified (approximate) form of the heterogeneity model is a compact, closed-form probit function that can readily be fitted to clinical series by conventional maximum-likelihood methodology. This heterogeneity model provides a slightly better fit to the datasets than the conventional LQ model, with the same numbers of fitted parameters. The parameter estimates of the clinically

A parallel adaptive finite element simplified spherical harmonics approximation solver for frequency domain fluorescence molecular imaging

International Nuclear Information System (INIS)

Lu Yujie; Zhu Banghe; Rasmussen, John C; Sevick-Muraca, Eva M; Shen Haiou; Wang Ge

2010-01-01

Fluorescence molecular imaging/tomography may play an important future role in preclinical research and clinical diagnostics. Time- and frequency-domain fluorescence imaging can acquire more measurement information than the continuous wave (CW) counterpart, improving the image quality of fluorescence molecular tomography. Although diffusion approximation (DA) theory has been extensively applied in optical molecular imaging, high-order photon migration models need to be further investigated to match quantitation provided by nuclear imaging. In this paper, a frequency-domain parallel adaptive finite element solver is developed with simplified spherical harmonics (SP N ) approximations. To fully evaluate the performance of the SP N approximations, a fast time-resolved tetrahedron-based Monte Carlo fluorescence simulator suitable for complex heterogeneous geometries is developed using a convolution strategy to realize the simulation of the fluorescence excitation and emission. The validation results show that high-order SP N can effectively correct the modeling errors of the diffusion equation, especially when the tissues have high absorption characteristics or when high modulation frequency measurements are used. Furthermore, the parallel adaptive mesh evolution strategy improves the modeling precision and the simulation speed significantly on a realistic digital mouse phantom. This solver is a promising platform for fluorescence molecular tomography using high-order approximations to the radiative transfer equation.

Melting behavior of a model molecular crystalline GeI4

International Nuclear Information System (INIS)

Fuchizaki, Kazuhiro; Asano, Yuta

2015-01-01

A model molecular crystalline GeI 4 was examined using molecular dynamics simulation. The model was constructed in such a way that rigid tetrahedral molecules interact with each other via Lennard-Jones potentials whose centers are located at the vertices of a tetrahedron. Because no other interaction that can “soften” the intermolecular interaction was introduced, the melting curve of the model crystalline material does not exhibit the anomaly that was found for the real substance. However, the current investigation is useful in that it could settle the upper bound of pressure below which the model can predict properties of the molecular liquid. Moreover, singularity-free nature of the melting curve allowed us to analytically treat the melting curve in the light of the Kumari-Dass-Kechin equation. As a result, we could definitely conclude that the well-known Simon equation for the melting curve is merely an approximate expression. The condition for the validity of Simon’s equation was identified. (author)

Animal models for rotator cuff repair.

Science.gov (United States)

Lebaschi, Amir; Deng, Xiang-Hua; Zong, Jianchun; Cong, Guang-Ting; Carballo, Camila B; Album, Zoe M; Camp, Christopher; Rodeo, Scott A

2016-11-01

Rotator cuff (RC) injuries represent a significant source of pain, functional impairment, and morbidity. The large disease burden of RC pathologies necessitates rapid development of research methodologies to treat these conditions. Given their ability to model anatomic, biomechanical, cellular, and molecular aspects of the human RC, animal models have played an indispensable role in reducing injury burden and advancing this field of research for many years. The development of animal models in the musculoskeletal (MSK) research arena is uniquely different from that in other fields in that the similarity of macrostructures and functions is as critical to replicate as cellular and molecular functions. Traditionally, larger animals have been used because of their anatomic similarity to humans and the ease of carrying out realistic surgical procedures. However, refinement of current molecular methods, introduction of novel research tools, and advancements in microsurgical techniques have increased the applicability of small animal models in MSK research. In this paper, we review RC animal models and emphasize a murine model that may serve as a valuable instrument for future RC tendon repair investigations. © 2016 New York Academy of Sciences.

Effective realistic interactions for low momentum Hilbert spaces

International Nuclear Information System (INIS)

Weber, Dennis

2012-01-01

Realistic nucleon-nucleon potentials are an essential ingredient of modern microscopic many-body calculations. These potentials can be represented in two different ways: operator representation or matrix element representation. In operator representation the potential is represented by a set of quantum mechanical operators while in matrix element representation it is defined by the matrix elements in a given basis. Many modern potentials are constructed directly in matrix element representation. While the matrix element representation can be calculated from the operator representation, the determination of the operator representation from the matrix elements is more difficult. Some methods to solve the nuclear many-body problem, such as Fermionic Molecular Dynamics (FMD) or the Green's Function Monte Carlo (GFMC) method, however require explicitly the operator representation of the potential, as they do not work in a fixed many-body basis. It is therefore desirable to derive an operator representation also for the interactions given by matrix elements. In this work a method is presented which allows the derivation of an approximate operator representation starting from the momentum space partial wave matrix elements of the interaction. For that purpose an ansatz for the operator representation is chosen. The parameters in the ansatz are determined by a fit to the partial wave matrix elements. Since a perfect reproduction of the matrix elements in general cannot be achieved with a finite number of operators and the quality of the results depends on the choice of the ansatz, the obtained operator representation is tested in nuclear many-body calculations and the results are compared with those from the initial interaction matrix elements. For the calculation of the nucleon-nucleon scattering phase shifts and the deuteron properties a computer code written within this work is used. For larger nuclei the No Core Shell Model (NCSM) and FMD are applied. The described

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

Science.gov (United States)

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

2017-03-01

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

Separable expansion for realistic multichannel scattering problems

International Nuclear Information System (INIS)

Canton, L.; Cattapan, G.; Pisent, G.

1987-01-01

A new approach to the multichannel scattering problem with realistic local or nonlocal interactions is developed. By employing the negative-energy solutions of uncoupled Sturmian eigenvalue problems referring to simple auxiliary potentials, the coupling interactions appearing to the original multichannel problem are approximated by finite-rank potentials. By resorting to integral-equation tecniques the coupled-channel equations are then reduced to linear algebraic equations which can be straightforwardly solved. Compact algebraic expressions for the relevant scattering matrix elements are thus obtained. The convergence of the method is tasted in the single-channel case with realistic optical potentials. Excellent agreement is obtained with a few terms in the separable expansion for both real and absorptive interactions

Realistic nurse-led policy implementation, optimization and evaluation: novel methodological exemplar.

Science.gov (United States)

Noyes, Jane; Lewis, Mary; Bennett, Virginia; Widdas, David; Brombley, Karen

2014-01-01

To report the first large-scale realistic nurse-led implementation, optimization and evaluation of a complex children's continuing-care policy. Health policies are increasingly complex, involve multiple Government departments and frequently fail to translate into better patient outcomes. Realist methods have not yet been adapted for policy implementation. Research methodology - Evaluation using theory-based realist methods for policy implementation. An expert group developed the policy and supporting tools. Implementation and evaluation design integrated diffusion of innovation theory with multiple case study and adapted realist principles. Practitioners in 12 English sites worked with Consultant Nurse implementers to manipulate the programme theory and logic of new decision-support tools and care pathway to optimize local implementation. Methods included key-stakeholder interviews, developing practical diffusion of innovation processes using key-opinion leaders and active facilitation strategies and a mini-community of practice. New and existing processes and outcomes were compared for 137 children during 2007-2008. Realist principles were successfully adapted to a shorter policy implementation and evaluation time frame. Important new implementation success factors included facilitated implementation that enabled 'real-time' manipulation of programme logic and local context to best-fit evolving theories of what worked; using local experiential opinion to change supporting tools to more realistically align with local context and what worked; and having sufficient existing local infrastructure to support implementation. Ten mechanisms explained implementation success and differences in outcomes between new and existing processes. Realistic policy implementation methods have advantages over top-down approaches, especially where clinical expertise is low and unlikely to diffuse innovations 'naturally' without facilitated implementation and local optimization. © 2013

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

Science.gov (United States)

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

2016-09-01

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

Does preliminary optimisation of an anatomically correct skull-brain model using simple simulants produce clinically realistic ballistic injury fracture patterns?

Science.gov (United States)

Mahoney, P F; Carr, D J; Delaney, R J; Hunt, N; Harrison, S; Breeze, J; Gibb, I

2017-07-01

Ballistic head injury remains a significant threat to military personnel. Studying such injuries requires a model that can be used with a military helmet. This paper describes further work on a skull-brain model using skulls made from three different polyurethane plastics and a series of skull 'fills' to simulate brain (3, 5, 7 and 10% gelatine by mass and PermaGel™). The models were subjected to ballistic impact from 7.62 × 39 mm mild steel core bullets. The first part of the work compares the different polyurethanes (mean bullet muzzle velocity of 708 m/s), and the second part compares the different fills (mean bullet muzzle velocity of 680 m/s). The impact events were filmed using high speed cameras. The resulting fracture patterns in the skulls were reviewed and scored by five clinicians experienced in assessing penetrating head injury. In over half of the models, one or more assessors felt aspects of the fracture pattern were close to real injury. Limitations of the model include the skull being manufactured in two parts and the lack of a realistic skin layer. Further work is ongoing to address these.

From Minimal to Realistic Supersymmetric SU(5) Grand Unification

CERN Document Server

Altarelli, Guido; Masina, I; Altarelli, Guido; Feruglio, Ferruccio; Masina, Isabella

2000-01-01

We construct and discuss a "realistic" example of SUSY SU(5) GUT model, with an additional U(1) flavour symmetry, that is not plagued by the need of large fine tunings, like those associated with doublet-triplet splitting in the minimal model, and that leads to an acceptable phenomenology. This includes coupling unification with a value of alpha_s(m_Z) in much better agreement with the data than in the minimal version, an acceptable hierarchical pattern for fermion masses and mixing angles, also including neutrino masses and mixings, and a proton decay rate compatible with present limits (but the discovery of proton decay should be within reach of the next generation of experiments). In the neutrino sector the preferred solution is one with nearly maximal mixing both for atmospheric and solar neutrinos.

Grid computing in large pharmaceutical molecular modeling.

Science.gov (United States)

Claus, Brian L; Johnson, Stephen R

2008-07-01

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

The construction of 'realistic' four-dimensional strings through orbifolds

International Nuclear Information System (INIS)

Font, A.; Quevedo, F.; Sierra, A.

1990-01-01

We discuss the construction of 'realistic' lower rank 4-dimensional strings, through symmetric orbifolds with background fields. We present Z 3 three-generation SU(3)xSU(2)xU(1) models as well as models incorporating a left-right SU(2) L xSU(2) R xU(1) B-L symmetry in which proton stability is automatically guaranteed. Conformal field theory selection rules are used to find the flat directions to all orders which lead to these low-rank models and to study the relevant Yukawa couplings. A hierarchical structure of quark-lepton masses appears naturally in some models. We also present a detailed study of the structure of the Z 3 xZ 3 orbifold including the generalized GSO projection, the effect of discrete torsion and the conformal field theory Yukawa coupling selection rules. All these points are illustrated with a three-generation Z 3 xZ 3 model. We have made an effort to write a self-contained presentation in order to make this material available to non-string experts interested in the phenomenological aspects of this theory. (orig.)

The construction of ``realistic'' four-dimensional strings through orbifolds

Science.gov (United States)

Font, A.; Ibáñez, L. E.; Quevedo, F.; Sierra, A.

1990-02-01

We discuss the construction of "realistic" lower rank 4-dimensional strings, through symmetric orbifolds with background fields. We present Z 3 three-generation SU(3) × SU(2) × U(1) models as well as models incorporating a left-right SU(2) L × SU(2) R × U(1) B-L symmetry in which proton stability is automatically guaranteed. Conformal field theory selection rules are used to find the flat directions to all orders which lead to these low-rank models and to study the relevant Yukawa couplings. A hierarchical structure of quark-lepton masses appears naturally in some models. We also present a detailed study of the structure of the Z 3 × Z 3 orbifold including the generalized GSO projection, the effect of discrete torsion and the conformal field theory Yukawa coupling selection rules. All these points are illustrated with a three-generation Z 3 × Z 3 model. We have made an effort to write a self-contained presentation in order to make this material available to non-string experts interested in the phenomenological aspects of this theory.

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

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Hepburn Iain

2012-05-01

Full Text Available Abstract Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins, conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

Science.gov (United States)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

Quantifying introgression risk with realistic population genetics.

Science.gov (United States)

Ghosh, Atiyo; Meirmans, Patrick G; Haccou, Patsy

2012-12-07

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.

Automatic skull segmentation from MR images for realistic volume conductor models of the head: Assessment of the state-of-the-art.

Science.gov (United States)

Nielsen, Jesper D; Madsen, Kristoffer H; Puonti, Oula; Siebner, Hartwig R; Bauer, Christian; Madsen, Camilla Gøbel; Saturnino, Guilherme B; Thielscher, Axel

2018-03-12

Anatomically realistic volume conductor models of the human head are important for accurate forward modeling of the electric field during transcranial brain stimulation (TBS), electro- (EEG) and magnetoencephalography (MEG). In particular, the skull compartment exerts a strong influence on the field distribution due to its low conductivity, suggesting the need to represent its geometry accurately. However, automatic skull reconstruction from structural magnetic resonance (MR) images is difficult, as compact bone has a very low signal in magnetic resonance imaging (MRI). Here, we evaluate three methods for skull segmentation, namely FSL BET2, the unified segmentation routine of SPM12 with extended spatial tissue priors, and the skullfinder tool of BrainSuite. To our knowledge, this study is the first to rigorously assess the accuracy of these state-of-the-art tools by comparison with CT-based skull segmentations on a group of ten subjects. We demonstrate several key factors that improve the segmentation quality, including the use of multi-contrast MRI data, the optimization of the MR sequences and the adaptation of the parameters of the segmentation methods. We conclude that FSL and SPM12 achieve better skull segmentations than BrainSuite. The former methods obtain reasonable results for the upper part of the skull when a combination of T1- and T2-weighted images is used as input. The SPM12-based results can be improved slightly further by means of simple morphological operations to fix local defects. In contrast to FSL BET2, the SPM12-based segmentation with extended spatial tissue priors and the BrainSuite-based segmentation provide coarse reconstructions of the vertebrae, enabling the construction of volume conductor models that include the neck. We exemplarily demonstrate that the extended models enable a more accurate estimation of the electric field distribution during transcranial direct current stimulation (tDCS) for montages that involve extraencephalic

Cohesion between two clay lamellae: From Primitive Model to Full Molecular Simulation

International Nuclear Information System (INIS)

Carrier, Benoit; Vandamme, Matthieu; Pellenq, Roland; Van Damme, Henri

2012-01-01

Document available in extended abstract form only. The objective of this work is to investigate the range of validity of various models to describe accurately the cohesion between two charged clay lamellae. These models, in order of increasing complexity, are the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the primitive model, the explicit solvent primitive model and the full molecular model. We aim at providing a clear picture of which physical mechanisms play a significant role for various interlayer spacings, surface charges and cationic charges. The up-scaling of the mechanical properties starting from the lamellar microstructure of a smectite is usually performed within the framework of the DLVO theory. In this case, the interaction between two charged lamellae with cations between them is the sum of the repulsive double layer electrostatic interaction and of the attractive Van der Waals interaction. However, the Primitive Model shows that concentration fluctuations of counter-ions can generate a strongly attractive ionic correlation force. The Primitive Model is a Monte-Carlo simulation of hydrated counter-ions between two infinite charges surfaces and the water is implicitly modeled by scaling all electrostatic interactions by the dielectric permittivity of bulk water. Nevertheless, for very small inter-layer spacings (1 nm), molecular simulations and experiments show that water is organized in a layered structure and does not behave like bulk water. Therefore, we investigate the role of the solvent in the cohesion of clay lamellae. For this purpose, we use a modified version of the original Primitive Model in which the solvent is modeled by point-dipoles: This model is called the Explicit Solvent Primitive Model. We consider four different systems: A Na + -montmorillonite, a Ca 2+ -montmorillonite, a Na + -vermiculite, a Ca 2+ -vermiculite. The vermiculite layers are twice as charged as the montmorillonite layers. We use a full molecular model as a

Lessons learned in using realist evaluation to assess maternal and newborn health programming in rural Bangladesh.

Science.gov (United States)

Adams, Alayne; Sedalia, Saroj; McNab, Shanon; Sarker, Malabika

2016-03-01

Realist evaluation furnishes valuable insight to public health practitioners and policy makers about how and why interventions work or don't work. Moving beyond binary measures of success or failure, it provides a systematic approach to understanding what goes on in the 'Black Box' and how implementation decisions in real life contexts can affect intervention effectiveness. This paper reflects on an experience in applying the tenets of realist evaluation to identify optimal implementation strategies for scale-up of Maternal and Newborn Health (MNH) programmes in rural Bangladesh. Supported by UNICEF, the three MNH programmes under consideration employed different implementation models to deliver similar services and meet similar MNH goals. Programme targets included adoption of recommended antenatal, post-natal and essential newborn care practices; health systems strengthening through improved referral, accountability and administrative systems, and increased community knowledge. Drawing on focused examples from this research, seven steps for operationalizing the realist evaluation approach are offered, while emphasizing the need to iterate and innovate in terms of methods and analysis strategies. The paper concludes by reflecting on lessons learned in applying realist evaluation, and the unique insights it yields regarding implementation strategies for successful MNH programming. © The Author 2015. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Fatigue - determination of a more realistic usage factor

International Nuclear Information System (INIS)

Lang, H.

2001-01-01

The ability to use a suitable counting method for determining the stress range spectrum in elastic and simplified elastic-plastic fatigue analyses is of crucial importance for enabling determination of a realistic usage factor. Determination of elastic-plastic strain range using the K e factor from fictitious elastically calculated loads is also important in the event of elastic behaviour being exceeded. This paper thus examines both points in detail. A fatigue module with additional options, which functions on this basis is presented. The much more realistic determination of usage factor presented here offers various economic benefits depending on the application

The effects of presenting multidigit mathematics problems in a realistic context on sixth graders' problem solving

NARCIS (Netherlands)

Hickendorff, M.

2013-01-01

Mathematics education and assessments increasingly involve arithmetic problems presented in context: a realistic situation that requires mathematical modeling. This study assessed the effects of such typical school mathematics contexts on two aspects of problem solving: performance and strategy use.

Motor properties from persistence: a linear molecular walker lacking spatial and temporal asymmetry

International Nuclear Information System (INIS)

Zuckermann, Martin J; Forde, Nancy R; Angstmann, Christopher N; Schmitt, Regina; Linke, Heiner; Blab, Gerhard A; Bromley, Elizabeth HC; Curmi, Paul MG

2015-01-01

The stepping direction of linear molecular motors is usually defined by a spatial asymmetry of the motor, its track, or both. Here we present a model for a molecular walker that undergoes biased directional motion along a symmetric track in the presence of a temporally symmetric chemical cycle. Instead of using asymmetry, directionality is achieved by persistence. At small load force the walker can take on average thousands of steps in a given direction until it stochastically reverses direction. We discuss a specific experimental implementation of a synthetic motor based on this design and find, using Langevin and Monte Carlo simulations, that a realistic walker can work against load forces on the order of picoNewtons with an efficiency of ∼18%, comparable to that of kinesin. In principle, the walker can be turned into a permanent motor by externally monitoring the walker’s momentary direction of motion, and using feedback to adjust the direction of a load force. We calculate the thermodynamic cost of using feedback to enhance motor performance in terms of the Shannon entropy, and find that it reduces the efficiency of a realistic motor only marginally. We discuss the implications for natural protein motor performance in the context of the strong performance of this design based only on a thermal ratchet. (paper)

Realistic rhetoric and legal decision

Directory of Open Access Journals (Sweden)

João Maurício Adeodato

2017-06-01

Full Text Available The text aims to lay the foundations of a realistic rhetoric, from the descriptive perspective of how the legal decision actually takes place, without normative considerations. Aristotle's rhetorical idealism and its later prestige reduced rhetoric to the art of persuasion, eliminating important elements of sophistry, especially with regard to legal decision. It concludes with a rhetorical perspective of judicial activism in complex societies.

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

Radiative transitions from Υ(5S) to molecular bottomonium

International Nuclear Information System (INIS)

Voloshin, M. B.

2011-01-01

The heavy quark spin symmetry implies that in addition to the recently observed Z(10610) and Z(10650) molecular resonances with I G =1 + , there should exist two or four molecular bottomonium-like states with I G =1 - . Properties of these G-odd states are considered, including their production in the radiative transitions from Υ(5S), by applying the same symmetry to the Υ(5S) resonance and the transition amplitudes. The considered radiative processes can provide a realistic option for observing the yet hypothetical states.

Bayesian semiparametric regression models to characterize molecular evolution

Directory of Open Access Journals (Sweden)

Datta Saheli

2012-10-01

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

Determination of Realistic Fire Scenarios in Spacecraft

Science.gov (United States)

Dietrich, Daniel L.; Ruff, Gary A.; Urban, David

2013-01-01

This paper expands on previous work that examined how large a fire a crew member could successfully survive and extinguish in the confines of a spacecraft. The hazards to the crew and equipment during an accidental fire include excessive pressure rise resulting in a catastrophic rupture of the vehicle skin, excessive temperatures that burn or incapacitate the crew (due to hyperthermia), carbon dioxide build-up or accumulation of other combustion products (e.g. carbon monoxide). The previous work introduced a simplified model that treated the fire primarily as a source of heat and combustion products and sink for oxygen prescribed (input to the model) based on terrestrial standards. The model further treated the spacecraft as a closed system with no capability to vent to the vacuum of space. The model in the present work extends this analysis to more realistically treat the pressure relief system(s) of the spacecraft, include more combustion products (e.g. HF) in the analysis and attempt to predict the fire spread and limiting fire size (based on knowledge of terrestrial fires and the known characteristics of microgravity fires) rather than prescribe them in the analysis. Including the characteristics of vehicle pressure relief systems has a dramatic mitigating effect by eliminating vehicle overpressure for all but very large fires and reducing average gas-phase temperatures.

Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

KAUST Repository

Kaushik, Ananth P.; Clancy, Paulette

2012-01-01

We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well

A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

Science.gov (United States)

Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

2011-01-01

Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

Applications of Molecular and Materials Modeling

Science.gov (United States)

2002-01-01

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

A realistic large-scale model of the cerebellum granular layer predicts circuit spatio-temporal filtering properties

Directory of Open Access Journals (Sweden)

Sergio Solinas

2010-05-01

Full Text Available The way the cerebellar granular layer transforms incoming mossy fiber signals into new spike patterns to be related to Purkinje cells is not yet clear. Here, a realistic computational model of the granular layer was developed and used to address four main functional hypotheses: center-surround organization, time-windowing, high-pass filtering in responses to spike bursts and coherent oscillations in response to diffuse random activity. The model network was activated using patterns inspired by those recorded in vivo. Burst stimulation of a small mossy fiber bundle resulted in granule cell bursts delimited in time (time windowing and space (center-surround by network inhibition. This burst-burst transmission showed marked frequency-dependence configuring a high-pass filter with cut-off frequency around 100 Hz. The contrast between center and surround properties was regulated by the excitatory-inhibitory balance. The stronger excitation made the center more responsive to 10-50 Hz input frequencies and enhanced the granule cell output (with spike occurring earlier and with higher frequency and number compared to the surround. Finally, over a certain level of mossy fiber background activity, the circuit generated coherent oscillations in the theta-frequency band. All these processes were fine-tuned by NMDA and GABA-A receptor activation and neurotransmitter vesicle cycling in the cerebellar glomeruli. This model shows that available knowledge on cellular mechanisms is sufficient to unify the main functional hypotheses on the cerebellum granular layer and suggests that this network can behave as an adaptable spatio-temporal filter coordinated by theta-frequency oscillations.

A molecular prognostic model predicts esophageal squamous cell carcinoma prognosis.

Directory of Open Access Journals (Sweden)

Hui-Hui Cao

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

Substrate binding and catalytic mechanism in phospholipase C from Bacillus cereus. a molecular mechanics and molecular dynamics study

DEFF Research Database (Denmark)

da Graça Thrige, D; Buur, J R; Jørgensen, Flemming Steen

1997-01-01

cereus including a docked substrate molecule was subjected to a stepwise molecular mechanics energy minimization. Second, the location of the nucleophilic water molecule in the active site of the fully relaxed enzyme-substrate complex was determined by evaluation of nonbonded interaction energies between...... water molecule was verified during a 100 ps molecular dynamics simulation. During the simulation the substrate undergoes a conformational change, but retains its localization in the active site. The contacts between the enzyme, the substrate, and the nucleophilic water molecule display some fluctuations...... the strong electrostatic interactions in the active site realistically during energy minimization, delocalization of the charges from the three zinc ions was considered. Therefore, quantum mechanics calculations on the zinc ions and the zinc-coordinating residues were carried out prior to the molecular...

Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

Energy Technology Data Exchange (ETDEWEB)

Hepburn, I.; De Schutter, E., E-mail: erik@oist.jp [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan); Theoretical Neurobiology & Neuroengineering, University of Antwerp, Antwerp 2610 (Belgium); Chen, W. [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan)

2016-08-07

Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

Protocol for an HTA report: Does therapeutic writing help people with long-term conditions? Systematic review, realist synthesis and economic modelling.

Science.gov (United States)

Meads, C; Nyssen, O P; Wong, G; Steed, L; Bourke, L; Ross, C A; Hayman, S; Field, V; Lord, J; Greenhalgh, T; Taylor, S J C

2014-02-18

Long-term medical conditions (LTCs) cause reduced health-related quality of life and considerable health service expenditure. Writing therapy has potential to improve physical and mental health in people with LTCs, but its effectiveness is not established. This project aims to establish the clinical and cost-effectiveness of therapeutic writing in LTCs by systematic review and economic evaluation, and to evaluate context and mechanisms by which it might work, through realist synthesis. Included are any comparative study of therapeutic writing compared with no writing, waiting list, attention control or placebo writing in patients with any diagnosed LTCs that report at least one of the following: relevant clinical outcomes; quality of life; health service use; psychological, behavioural or social functioning; adherence or adverse events. Searches will be conducted in the main medical databases including MEDLINE, EMBASE, PsycINFO, The Cochrane Library and Science Citation Index. For the realist review, further purposive and iterative searches through snowballing techniques will be undertaken. Inclusions, data extraction and quality assessment will be in duplicate with disagreements resolved through discussion. Quality assessment will include using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. Data synthesis will be narrative and tabular with meta-analysis where appropriate. De novo economic modelling will be attempted in one clinical area if sufficient evidence is available and performed according to the National Institute for Health and Care Excellence (NICE) reference case.

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

Science.gov (United States)

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

2011-07-01

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

Modeling ion sensing in molecular electronics

International Nuclear Information System (INIS)

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

2014-01-01

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

Molecular modelling and radiopharmaceutical design

International Nuclear Information System (INIS)

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

2002-01-01

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

Photo-Realistic Image Synthesis and Virtual Cinematography

DEFF Research Database (Denmark)

Livatino, Salvatore

2005-01-01

Realistic Virtual View Synthesis is a new field of research that has received increasing attention in recent years. It is strictly related to the grown popularity of virtual reality and the spread of its applications, among which virtual photography and cinematography. The use of computer generated...... characters, "virtual actors", in the motion picture production increases every day. While the most known computer graphics techniques have largely been adopted successfully in nowadays fictions, it still remains very challenging to implement virtual actors which would resemble, visually, human beings....... Interestingly, film directors have been looking at the recent progress achieved by the research community in the field of realistic visualization of virtual views, and they have successfully implemented state of the art research approaches in their productions. An innovative concept is then gaining consensus...

Generating Geospatially Realistic Driving Patterns Derived From Clustering Analysis Of Real EV Driving Data

DEFF Research Database (Denmark)

Pedersen, Anders Bro; Aabrandt, Andreas; Østergaard, Jacob

2014-01-01

In order to provide a vehicle fleet that realistically represents the predicted Electric Vehicle (EV) penetration for the future, a model is required that mimics people driving behaviour rather than simply playing back collected data. When the focus is broadened from on a traditional user...... scales, which calls for a statistically correct, yet flexible model. This paper describes a method for modelling EV, based on non-categorized data, which takes into account the plug in locations of the vehicles. By using clustering analysis to extrapolate and classify the primary locations where...

Spiral-wave dynamics in ionically realistic mathematical models for human ventricular tissue: the effects of periodic deformation.

Science.gov (United States)

Nayak, Alok R; Pandit, Rahul

2014-01-01

We carry out an extensive numerical study of the dynamics of spiral waves of electrical activation, in the presence of periodic deformation (PD) in two-dimensional simulation domains, in the biophysically realistic mathematical models of human ventricular tissue due to (a) ten-Tusscher and Panfilov (the TP06 model) and (b) ten-Tusscher, Noble, Noble, and Panfilov (the TNNP04 model). We first consider simulations in cable-type domains, in which we calculate the conduction velocity θ and the wavelength λ of a plane wave; we show that PD leads to a periodic, spatial modulation of θ and a temporally periodic modulation of λ; both these modulations depend on the amplitude and frequency of the PD. We then examine three types of initial conditions for both TP06 and TNNP04 models and show that the imposition of PD leads to a rich variety of spatiotemporal patterns in the transmembrane potential including states with a single rotating spiral (RS) wave, a spiral-turbulence (ST) state with a single meandering spiral, an ST state with multiple broken spirals, and a state SA in which all spirals are absorbed at the boundaries of our simulation domain. We find, for both TP06 and TNNP04 models, that spiral-wave dynamics depends sensitively on the amplitude and frequency of PD and the initial condition. We examine how these different types of spiral-wave states can be eliminated in the presence of PD by the application of low-amplitude pulses by square- and rectangular-mesh suppression techniques. We suggest specific experiments that can test the results of our simulations.

Spiral-Wave Dynamics in Ionically Realistic MathematicalModels for Human Ventricular Tissue: The Effects of PeriodicDeformation

Directory of Open Access Journals (Sweden)

Alok Ranjan Nayak

2014-06-01

Full Text Available We carry out an extensive numerical study of the dynamics of spiral waves of electrical activation, in the presence of periodic deformation (PD in two-dimensional simulation domains, in the biophysically realistic mathematical models of human ventricular tissue due to (a ten-Tusscher and Panfilov (the TP06 model and (b ten-Tusscher, Noble, Noble, and Panfilov (theTNNP04 model. We first consider simulations in cable-type domains, in which we calculate the conduction velocity $CV$ andthe wavelength $lambda$ of a plane wave; we show that PD leads to a periodic, spatial modulation of $CV$ and a temporallyperiodic modulation of $lambda$; both these modulations depend on the amplitude and frequency of the PD. We then examine three types of initial conditions for both TP06 and TNNP04 models and show that the imposition of PD leads to a rich variety ofspatiotemporal patterns in the transmembrane potential including states with a single rotating spiral (RS wave, a spiral-turbulence (ST state with a single meandering spiral, an ST state with multiple broken spirals, and a state SA in which all spirals are absorbed at the boundaries of our simulation domain. We find, for both TP06 and TNNP04 models, that spiral-wave dynamics depends sensitively on the amplitude and frequency of PD and the initial condition. We examine how these different types of spiral-wave states can be eliminated in the presence of PD by the application of low-amplitude pulses on square and rectangular control meshes. We suggest specific experiments that can test the results of our simulations.

Metastable cosmic strings in realistic models

International Nuclear Information System (INIS)

Holman, R.

1992-01-01

The stability of the electroweak Z-string is investigated at high temperatures. The results show that, while finite temperature corrections can improve the stability of the Z-string, their effect is not strong enough to stabilize the Z-string in the standard electroweak model. Consequently, the Z-string will be unstable even under the conditions present during the electroweak phase transition. Phenomenologically viable models based on the gauge group SU(2) L x SU(2) R x U(1) B-L are then considered, and it is shown that metastable strings exist and are stable to small perturbations for a large region of the parameter space for these models. It is also shown that these strings are superconducting with bosonic charge carriers. The string superconductivity may be able to stabilize segments and loops against dynamical contraction. Possible implications of these strings for cosmology are discussed

I-Love relations for incompressible stars and realistic stars

Science.gov (United States)

Chan, T. K.; Chan, AtMa P. O.; Leung, P. T.

2015-02-01

In spite of the diversity in the equations of state of nuclear matter, the recently discovered I-Love-Q relations [Yagi and Yunes, Science 341, 365 (2013), 10.1126/science.1236462], which relate the moment of inertia, tidal Love number (deformability), and the spin-induced quadrupole moment of compact stars, hold for various kinds of realistic neutron stars and quark stars. While the physical origin of such universality is still a current issue, the observation that the I-Love-Q relations of incompressible stars can well approximate those of realistic compact stars hints at a new direction to approach the problem. In this paper, by establishing recursive post-Minkowskian expansion for the moment of inertia and the tidal deformability of incompressible stars, we analytically derive the I-Love relation for incompressible stars and show that the so-obtained formula can be used to accurately predict the behavior of realistic compact stars from the Newtonian limit to the maximum mass limit.

Blue Energy and Desalination with Nanoporous Carbon Electrodes: Capacitance from Molecular Simulations to Continuous Models

Directory of Open Access Journals (Sweden)

Michele Simoncelli

2018-04-01

Full Text Available Capacitive mixing (CapMix and capacitive deionization (CDI are currently developed as alternatives to membrane-based processes to harvest blue energy—from salinity gradients between river and sea water—and to desalinate water—using charge-discharge cycles of capacitors. Nanoporous electrodes increase the contact area with the electrolyte and hence, in principle, also the performance of the process. However, models to design and optimize devices should be used with caution when the size of the pores becomes comparable to that of ions and water molecules. Here, we address this issue by simulating realistic capacitors based on aqueous electrolytes and nanoporous carbide-derived carbon (CDC electrodes, accounting for both their complex structure and their polarization by the electrolyte under applied voltage. We compute the capacitance for two salt concentrations and validate our simulations by comparison with cyclic voltammetry experiments. We discuss the predictions of Debye-Hückel and Poisson-Boltzmann theories, as well as modified Donnan models, and we show that the latter can be parametrized using the molecular simulation results at high concentration. This then allows us to extrapolate the capacitance and salt adsorption capacity at lower concentrations, which cannot be simulated, finding a reasonable agreement with the experimental capacitance. We analyze the solvation of ions and their confinement within the electrodes—microscopic properties that are much more difficult to obtain experimentally than the electrochemical response but very important to understand the mechanisms at play. We finally discuss the implications of our findings for CapMix and CDI, both from the modeling point of view and from the use of CDCs in these contexts.

Blue Energy and Desalination with Nanoporous Carbon Electrodes: Capacitance from Molecular Simulations to Continuous Models

Science.gov (United States)

Simoncelli, Michele; Ganfoud, Nidhal; Sene, Assane; Haefele, Matthieu; Daffos, Barbara; Taberna, Pierre-Louis; Salanne, Mathieu; Simon, Patrice; Rotenberg, Benjamin

2018-04-01

Capacitive mixing (CapMix) and capacitive deionization (CDI) are currently developed as alternatives to membrane-based processes to harvest blue energy—from salinity gradients between river and sea water—and to desalinate water—using charge-discharge cycles of capacitors. Nanoporous electrodes increase the contact area with the electrolyte and hence, in principle, also the performance of the process. However, models to design and optimize devices should be used with caution when the size of the pores becomes comparable to that of ions and water molecules. Here, we address this issue by simulating realistic capacitors based on aqueous electrolytes and nanoporous carbide-derived carbon (CDC) electrodes, accounting for both their complex structure and their polarization by the electrolyte under applied voltage. We compute the capacitance for two salt concentrations and validate our simulations by comparison with cyclic voltammetry experiments. We discuss the predictions of Debye-Hückel and Poisson-Boltzmann theories, as well as modified Donnan models, and we show that the latter can be parametrized using the molecular simulation results at high concentration. This then allows us to extrapolate the capacitance and salt adsorption capacity at lower concentrations, which cannot be simulated, finding a reasonable agreement with the experimental capacitance. We analyze the solvation of ions and their confinement within the electrodes—microscopic properties that are much more difficult to obtain experimentally than the electrochemical response but very important to understand the mechanisms at play. We finally discuss the implications of our findings for CapMix and CDI, both from the modeling point of view and from the use of CDCs in these contexts.

Hyper-realistic face masks: a new challenge in person identification.

Science.gov (United States)

Sanders, Jet Gabrielle; Ueda, Yoshiyuki; Minemoto, Kazusa; Noyes, Eilidh; Yoshikawa, Sakiko; Jenkins, Rob

2017-01-01

We often identify people using face images. This is true in occupational settings such as passport control as well as in everyday social environments. Mapping between images and identities assumes that facial appearance is stable within certain bounds. For example, a person's apparent age, gender and ethnicity change slowly, if at all. It also assumes that deliberate changes beyond these bounds (i.e., disguises) would be easy to spot. Hyper-realistic face masks overturn these assumptions by allowing the wearer to look like an entirely different person. If unnoticed, these masks break the link between facial appearance and personal identity, with clear implications for applied face recognition. However, to date, no one has assessed the realism of these masks, or specified conditions under which they may be accepted as real faces. Herein, we examined incidental detection of unexpected but attended hyper-realistic masks in both photographic and live presentations. Experiment 1 (UK; n = 60) revealed no evidence for overt detection of hyper-realistic masks among real face photos, and little evidence of covert detection. Experiment 2 (Japan; n = 60) extended these findings to different masks, mask-wearers and participant pools. In Experiment 3 (UK and Japan; n = 407), passers-by failed to notice that a live confederate was wearing a hyper-realistic mask and showed limited evidence of covert detection, even at close viewing distance (5 vs. 20 m). Across all of these studies, viewers accepted hyper-realistic masks as real faces. Specific countermeasures will be required if detection rates are to be improved.

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.

Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

Science.gov (United States)

Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

2017-09-01

Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

Entropy stable modeling of non-isothermal multi-component diffuse-interface two-phase flows with realistic equations of state

KAUST Repository

Kou, Jisheng

2018-02-25

In this paper, we consider mathematical modeling and numerical simulation of non-isothermal compressible multi-component diffuse-interface two-phase flows with realistic equations of state. A general model with general reference velocity is derived rigorously through thermodynamical laws and Onsager\\'s reciprocal principle, and it is capable of characterizing compressibility and partial miscibility between multiple fluids. We prove a novel relation among the pressure, temperature and chemical potentials, which results in a new formulation of the momentum conservation equation indicating that the gradients of chemical potentials and temperature become the primary driving force of the fluid motion except for the external forces. A key challenge in numerical simulation is to develop entropy stable numerical schemes preserving the laws of thermodynamics. Based on the convex-concave splitting of Helmholtz free energy density with respect to molar densities and temperature, we propose an entropy stable numerical method, which solves the total energy balance equation directly, and thus, naturally satisfies the first law of thermodynamics. Unconditional entropy stability (the second law of thermodynamics) of the proposed method is proved by estimating the variations of Helmholtz free energy and kinetic energy with time steps. Numerical results validate the proposed method.

Entropy stable modeling of non-isothermal multi-component diffuse-interface two-phase flows with realistic equations of state

KAUST Repository

Kou, Jisheng; Sun, Shuyu

2018-01-01

In this paper, we consider mathematical modeling and numerical simulation of non-isothermal compressible multi-component diffuse-interface two-phase flows with realistic equations of state. A general model with general reference velocity is derived rigorously through thermodynamical laws and Onsager's reciprocal principle, and it is capable of characterizing compressibility and partial miscibility between multiple fluids. We prove a novel relation among the pressure, temperature and chemical potentials, which results in a new formulation of the momentum conservation equation indicating that the gradients of chemical potentials and temperature become the primary driving force of the fluid motion except for the external forces. A key challenge in numerical simulation is to develop entropy stable numerical schemes preserving the laws of thermodynamics. Based on the convex-concave splitting of Helmholtz free energy density with respect to molar densities and temperature, we propose an entropy stable numerical method, which solves the total energy balance equation directly, and thus, naturally satisfies the first law of thermodynamics. Unconditional entropy stability (the second law of thermodynamics) of the proposed method is proved by estimating the variations of Helmholtz free energy and kinetic energy with time steps. Numerical results validate the proposed method.

Putting a Realistic Theory of Mind into Agency Theory

DEFF Research Database (Denmark)

Foss, Nicolai Juul; Stea, Diego

2014-01-01

Agency theory is one of the most important foundational theories in management research, but it rests on contestable cognitive assumptions. Specifically, the principal is assumed to hold a perfect (correct) theory regarding some of the content of the agent's mind, while he is entirely ignorant...... concerning other such content. More realistically, individuals have some limited access to the minds of others. We explore the implications for classical agency theory of realistic assumptions regarding the human potential for interpersonal sensemaking. We discuss implications for the design and management...

Realistic searches on stretched exponential networks

Indian Academy of Sciences (India)

We consider navigation or search schemes on networks which have a degree distribution of the form () ∝ exp(−). In addition, the linking probability is taken to be dependent on social distances and is governed by a parameter . The searches are realistic in the sense that not all search chains can be completed.

Fletcher-Reeves based Particle Swarm Optimization for prediction of molecular structure.

Science.gov (United States)

Agrawal, Shikha; Silakari, Sanjay

2014-04-01

The determination of the most stable conformers of a molecule can be formulated as a global optimization problem. Knowing the stable conformers of a molecule is important because it allows us to understand its properties and behavior based on its structure. The most stable conformation is that involving the global minimum of potential energy. The problem of finding this global minimum is highly complex, and is computationally difficult because of the number of local minima, which grows exponentially with molecular size. In this paper, we propose a hybrid approach combining Particle Swarm Optimization (PSO) and the Fletcher-Reeves algorithm to minimize the potential energy function. The proposed hybrid algorithm is applied to a simplified molecular potential energy function in problems with up to 100 degrees of freedom and also to a realistic potential energy function modeling a pseudoethane molecule. The computational results for both the cases show that the proposed method performs significantly better than the other algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-01-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

Results of recent calculations using realistic potentials

International Nuclear Information System (INIS)

Friar, J.L.

1987-01-01

Results of recent calculations for the triton using realistic potentials with strong tensor forces are reviewed, with an emphasis on progress made using the many different calculational schemes. Several test problems are suggested. 49 refs., 5 figs

Molecular dynamics simulations of ballistic He penetration into W fuzz

NARCIS (Netherlands)

Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

2016-01-01

Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

Directory of Open Access Journals (Sweden)

Filippo Pullara

2015-10-01

Full Text Available Standard Molecular Dynamics simulations (MD are usually performed under periodic boundary conditions using the well-established “Ewald summation”. This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells—important in many biological activities, such as protein cooperativity and physiological/pathological aggregation—are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum. When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.

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

Science.gov (United States)

Thomas, Marcus; Schwartz, Russell

2017-05-23

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

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...

Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

Science.gov (United States)

Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

2018-05-01

We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

Getting realistic; Endstation Demut

Energy Technology Data Exchange (ETDEWEB)

Meyer, J.P.

2004-01-28

The fuel cell hype of the turn of the millenium has reached its end. The industry is getting realistic. If at all, fuel cell systems for private single-family and multiple dwellings will not be available until the next decade. With a Europe-wide field test, Vaillant intends to advance the PEM technology. [German] Der Brennstoffzellen-Hype der Jahrtausendwende ist verfolgen. Die Branche uebt sich in Bescheidenheit. Die Marktreife der Systeme fuer Ein- und Mehrfamilienhaeuser wird - wenn ueberhaupt - wohl erst im naechsten Jahrzehnt erreicht sein. Vaillant will durch einen europaweiten Feldtest die Entwicklung der PEM-Technologie vorantreiben. (orig.)

HELIOSEISMOLOGY OF A REALISTIC MAGNETOCONVECTIVE SUNSPOT SIMULATION

International Nuclear Information System (INIS)

Braun, D. C.; Birch, A. C.; Rempel, M.; Duvall, T. L. Jr.

2012-01-01

We compare helioseismic travel-time shifts measured from a realistic magnetoconvective sunspot simulation using both helioseismic holography and time-distance helioseismology, and measured from real sunspots observed with the Helioseismic and Magnetic Imager instrument on board the Solar Dynamics Observatory and the Michelson Doppler Imager instrument on board the Solar and Heliospheric Observatory. We find remarkable similarities in the travel-time shifts measured between the methodologies applied and between the simulated and real sunspots. Forward modeling of the travel-time shifts using either Born or ray approximation kernels and the sound-speed perturbations present in the simulation indicates major disagreements with the measured travel-time shifts. These findings do not substantially change with the application of a correction for the reduction of wave amplitudes in the simulated and real sunspots. Overall, our findings demonstrate the need for new methods for inferring the subsurface structure of sunspots through helioseismic inversions.

Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

Science.gov (United States)

Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

2018-08-01

Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

Biophysically realistic minimal model of dopamine neuron

Science.gov (United States)

Oprisan, Sorinel

2008-03-01

We proposed and studied a new biophysically relevant computational model of dopaminergic neurons. Midbrain dopamine neurons are involved in motivation and the control of movement, and have been implicated in various pathologies such as Parkinson's disease, schizophrenia, and drug abuse. The model we developed is a single-compartment Hodgkin-Huxley (HH)-type parallel conductance membrane model. The model captures the essential mechanisms underlying the slow oscillatory potentials and plateau potential oscillations. The main currents involved are: 1) a voltage-dependent fast calcium current, 2) a small conductance potassium current that is modulated by the cytosolic concentration of calcium, and 3) a slow voltage-activated potassium current. We developed multidimensional bifurcation diagrams and extracted the effective domains of sustained oscillations. The model includes a calcium balance due to the fundamental importance of calcium influx as proved by simultaneous electrophysiological and calcium imaging procedure. Although there are significant evidences to suggest a partially electrogenic calcium pump, all previous models considered only elecrtogenic pumps. We investigated the effect of the electrogenic calcium pump on the bifurcation diagram of the model and compared our findings against the experimental results.

Energetics and efficiency of a molecular motor model

DEFF Research Database (Denmark)

C. Fogedby, Hans; Svane, Axel

2013-01-01

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

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

KAUST Repository

Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr

2017-01-01

The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from

Organization of lipids in the tear film: a molecular-level view.

Directory of Open Access Journals (Sweden)

Alicja Wizert

Full Text Available Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film.

A realistic validation study of a new nitrogen multiple-breath washout system.

Directory of Open Access Journals (Sweden)

Florian Singer

Full Text Available BACKGROUND: For reliable assessment of ventilation inhomogeneity, multiple-breath washout (MBW systems should be realistically validated. We describe a new lung model for in vitro validation under physiological conditions and the assessment of a new nitrogen (N(2MBW system. METHODS: The N(2MBW setup indirectly measures the N(2 fraction (F(N2 from main-stream carbon dioxide (CO(2 and side-stream oxygen (O(2 signals: F(N2 = 1-F(O2-F(CO2-F(Argon. For in vitro N(2MBW, a double chamber plastic lung model was filled with water, heated to 37°C, and ventilated at various lung volumes, respiratory rates, and F(CO2. In vivo N(2MBW was undertaken in triplets on two occasions in 30 healthy adults. Primary N(2MBW outcome was functional residual capacity (FRC. We assessed in vitro error (√[difference](2 between measured and model FRC (100-4174 mL, and error between tests of in vivo FRC, lung clearance index (LCI, and normalized phase III slope indices (S(acin and S(cond. RESULTS: The model generated 145 FRCs under BTPS conditions and various breathing patterns. Mean (SD error was 2.3 (1.7%. In 500 to 4174 mL FRCs, 121 (98% of FRCs were within 5%. In 100 to 400 mL FRCs, the error was better than 7%. In vivo FRC error between tests was 10.1 (8.2%. LCI was the most reproducible ventilation inhomogeneity index. CONCLUSION: The lung model generates lung volumes under the conditions encountered during clinical MBW testing and enables realistic validation of MBW systems. The new N(2MBW system reliably measures lung volumes and delivers reproducible LCI values.

The Development and Validation of an In Vitro Airway Model to Assess Realistic Airway Deposition and Drug Permeation Behavior of Orally Inhaled Products Across Synthetic Membranes.

Science.gov (United States)

Huynh, Bao K; Traini, Daniela; Farkas, Dale R; Longest, P Worth; Hindle, Michael; Young, Paul M

2018-04-01

Current in vitro approaches to assess lung deposition, dissolution, and cellular transport behavior of orally inhaled products (OIPs) have relied on compendial impactors to collect drug particles that are likely to deposit in the airway; however, the main drawback with this approach is that these impactors do not reflect the airway and may not necessarily represent drug deposition behavior in vivo. The aim of this article is to describe the development and method validation of a novel hybrid in vitro approach to assess drug deposition and permeation behavior in a more representative airway model. The medium-sized Virginia Commonwealth University (VCU) mouth-throat (MT) and tracheal-bronchial (TB) realistic upper airway models were used in this study as representative models of the upper airway. The TB model was modified to accommodate two Snapwell ® inserts above the first TB airway bifurcation region to collect deposited nebulized ciprofloxacin-hydrochloride (CIP-HCL) droplets as a model drug aerosol system. Permeation characteristics of deposited nebulized CIP-HCL droplets were assessed across different synthetic membranes using the Snapwell test system. The Snapwell test system demonstrated reproducible and discriminatory drug permeation profiles for already dissolved and nebulized CIP-HCL droplets through a range of synthetic permeable membranes under different test conditions. The rate and extent of drug permeation depended on the permeable membrane material used, presence of a stirrer in the receptor compartment, and, most importantly, the drug collection method. This novel hybrid in vitro approach, which incorporates a modified version of a realistic upper airway model, coupled with the Snapwell test system holds great potential to evaluate postairway deposition characteristics, such as drug permeation and particle dissolution behavior of OIPs. Future studies will expand this approach using a cell culture-based setup instead of synthetic membranes, within a

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

Science.gov (United States)

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

2015-12-01

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

Electronic shift register memory based on molecular electron-transfer reactions

Science.gov (United States)

Hopfield, J. J.; Onuchic, Jose Nelson; Beratan, David N.

1989-01-01

The design of a shift register memory at the molecular level is described in detail. The memory elements are based on a chain of electron-transfer molecules incorporated on a very large scale integrated (VLSI) substrate, and the information is shifted by photoinduced electron-transfer reactions. The design requirements for such a system are discussed, and several realistic strategies for synthesizing these systems are presented. The immediate advantage of such a hybrid molecular/VLSI device would arise from the possible information storage density. The prospect of considerable savings of energy per bit processed also exists. This molecular shift register memory element design solves the conceptual problems associated with integrating molecular size components with larger (micron) size features on a chip.

Two-Capacitor Problem: A More Realistic View.

Science.gov (United States)

Powell, R. A.

1979-01-01

Discusses the two-capacitor problem by considering the self-inductance of the circuit used and by determining how well the usual series RC circuit approximates the two-capacitor problem when realistic values of L, C, and R are chosen. (GA)

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Satellite Maps Deliver More Realistic Gaming

Science.gov (United States)

2013-01-01

When Redwood City, California-based Electronic Arts (EA) decided to make SSX, its latest snowboarding video game, it faced challenges in creating realistic-looking mountains. The solution was NASA's ASTER Global Digital Elevation Map, made available by the Jet Propulsion Laboratory, which EA used to create 28 real-life mountains from 9 different ranges for its award-winning game.

Molecular modeling of protonic acid doping of emeraldine base polyaniline for chemical sensors

NARCIS (Netherlands)

Chen, X.; Yuan, C.A.; Wong, C.K.Y.; Ye, H.; Leung, S.Y.Y.; Zhang, G.

2012-01-01

We proposed a molecular modeling methodology to study the protonic acid doping of emeraldine base polyaniline which can used in gas detection. The commercial forcefield COMPASS was used for the polymer and protonic acid molecules. The molecular model, which is capable of representing the polyaniline

Predicting perceptual quality of images in realistic scenario using deep filter banks

Science.gov (United States)

Zhang, Weixia; Yan, Jia; Hu, Shiyong; Ma, Yang; Deng, Dexiang

2018-03-01

Classical image perceptual quality assessment models usually resort to natural scene statistic methods, which are based on an assumption that certain reliable statistical regularities hold on undistorted images and will be corrupted by introduced distortions. However, these models usually fail to accurately predict degradation severity of images in realistic scenarios since complex, multiple, and interactive authentic distortions usually appear on them. We propose a quality prediction model based on convolutional neural network. Quality-aware features extracted from filter banks of multiple convolutional layers are aggregated into the image representation. Furthermore, an easy-to-implement and effective feature selection strategy is used to further refine the image representation and finally a linear support vector regression model is trained to map image representation into images' subjective perceptual quality scores. The experimental results on benchmark databases present the effectiveness and generalizability of the proposed model.

Molecular structure based property modeling: Development/ improvement of property models through a systematic property-data-model analysis

DEFF Research Database (Denmark)

Hukkerikar, Amol Shivajirao; Sarup, Bent; Sin, Gürkan

2013-01-01

models. To make the property-data-model analysis fast and efficient, an approach based on the “molecular structure similarity criteria” to identify molecules (mono-functional, bi-functional, etc.) containing specified set of structural parameters (that is, groups) is employed. The method has been applied...

The hierarchical structure of molecular clouds

International Nuclear Information System (INIS)

Chieze, J.P.

1987-01-01

The mass-radius-velocity dispersion relations observed among the members of cool molecular complexes is interpreted in terms of fragmentation at the gravitational instability threshold in a roughly constant pressure environment. The mass range of the self-similar fragmentation hierarchy is governed by the thermal instability thresholds. Using a realistic equation of state, the gravitational stability of thermally stable clumps is analysed as a function of both the local gas pressure and extinction of the mean interstellar radiation field

VHDL-AMS Simulation Framework for Molecular-FET Device-to-Circuit Modeling and Design

Directory of Open Access Journals (Sweden)

Mariagrazia Graziano

2018-01-01

Full Text Available We concentrate on Molecular-FET as a device and present a new modular framework based on VHDL-AMS. We have implemented different Molecular-FET models within the framework. The framework allows comparison between the models in terms of the capability to calculate accurate I-V characteristics. It also provides the option to analyze the impact of Molecular-FET and its implementation in the circuit with the extension of its use in an architecture based on the crossbar configuration. This analysis evidences the effect of choices of technological parameters, the ability of models to capture the impact of physical quantities, and the importance of considering defects at circuit fabrication level. The comparison tackles the computational efforts of different models and techniques and discusses the trade-off between accuracy and performance as a function of the circuit analysis final requirements. We prove this methodology using three different models and test them on a 16-bit tree adder included in Pentium 4 that, to the best of our knowledge, is the biggest circuits based on molecular device ever designed and analyzed.

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

Science.gov (United States)

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

2017-01-20

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

Protocol for an HTA report: Does therapeutic writing help people with long-term conditions? Systematic review, realist synthesis and economic modelling

Science.gov (United States)

Meads, C; Nyssen, O P; Wong, G; Steed, L; Bourke, L; Ross, C A; Hayman, S; Field, V; Lord, J; Greenhalgh, T; Taylor, S J C

2014-01-01

Introduction Long-term medical conditions (LTCs) cause reduced health-related quality of life and considerable health service expenditure. Writing therapy has potential to improve physical and mental health in people with LTCs, but its effectiveness is not established. This project aims to establish the clinical and cost-effectiveness of therapeutic writing in LTCs by systematic review and economic evaluation, and to evaluate context and mechanisms by which it might work, through realist synthesis. Methods Included are any comparative study of therapeutic writing compared with no writing, waiting list, attention control or placebo writing in patients with any diagnosed LTCs that report at least one of the following: relevant clinical outcomes; quality of life; health service use; psychological, behavioural or social functioning; adherence or adverse events. Searches will be conducted in the main medical databases including MEDLINE, EMBASE, PsycINFO, The Cochrane Library and Science Citation Index. For the realist review, further purposive and iterative searches through snowballing techniques will be undertaken. Inclusions, data extraction and quality assessment will be in duplicate with disagreements resolved through discussion. Quality assessment will include using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. Data synthesis will be narrative and tabular with meta-analysis where appropriate. De novo economic modelling will be attempted in one clinical area if sufficient evidence is available and performed according to the National Institute for Health and Care Excellence (NICE) reference case. PMID:24549165

Hierarchical modeling of molecular energies using a deep neural network

Science.gov (United States)

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

2018-06-01

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

Temperature effects on multiphase reactions of organic molecular markers: A modeling study

Science.gov (United States)

Pratap, Vikram; Chen, Ying; Yao, Guangming; Nakao, Shunsuke

2018-04-01

Various molecular markers are used in source apportionment studies. In early studies, molecular markers were assumed to be inert. However, recent studies suggest that molecular markers can decay rapidly through multiphase reactions, which makes interpretation of marker measurements challenging. This study presents a simplified model to account for the effects of temperature and relative humidity on the lifetime of molecular markers through a shift in gas-particle partitioning as well as a change in viscosity of the condensed phase. As a model case, this study examines the stability of levoglucosan, a key marker species of biomass burning, over a wide temperature range relevant to summertime and wintertime. Despite the importance of wood combustion for space heating in winter, the lifetime of levoglucosan in wintertime is not well understood. The model predicts that in low-temperature conditions, levoglucosan predominantly remains in the particle phase, and therefore its loss due to gas-phase oxidation reactions is significantly reduced. Furthermore, the movement of the levoglucosan from the bulk of the particle to the particle surface is reduced due to low diffusivity in the semi-solid state. The simplified model developed in this study reasonably reproduces upper and lower bounds of the lifetime of levoglucosan investigated in previous studies. The model results show that the levoglucosan depletion after seven days reduces significantly from ∼98% at 25 °C to marker (lifetime > 1 week) even at 60% relative humidity irrespective of the assumed fragility parameter D that controls estimated diffusivity. The model shows that lifetime of an organic molecular marker strongly depends on assumed D especially when a semi-volatile marker is in semi-solid organic aerosol.

Atomistic simulations of graphite etching at realistic time scales.

Science.gov (United States)

Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

2017-10-01

Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

The mechanical properties modeling of nano-scale materials by molecular dynamics

NARCIS (Netherlands)

Yuan, C.; Driel, W.D. van; Poelma, R.; Zhang, G.Q.

2012-01-01

We propose a molecular modeling strategy which is capable of mod-eling the mechanical properties on nano-scale low-dielectric (low-k) materials. Such modeling strategy has been also validated by the bulking force of carbon nano tube (CNT). This modeling framework consists of model generation method,

Realist cinema as world cinema

OpenAIRE

Nagib, Lucia

2017-01-01

The idea that “realism” is the common denominator across the vast range of productions normally labelled as “world cinema” is widespread and seemly uncontroversial. Leaving aside oppositional binaries that define world cinema as the other of Hollywood or of classical cinema, this chapter will test the realist premise by locating it in the mode of production. It will define this mode as an ethics that engages filmmakers, at cinema’s creative peaks, with the physical and historical environment,...

The importance of realistic dispersal models in conservation planning: application of a novel modelling platform to evaluate management scenarios in an Afrotropical biodiversity hotspot.

Science.gov (United States)

Aben, Job; Bocedi, Greta; Palmer, Stephen C F; Pellikka, Petri; Strubbe, Diederik; Hallmann, Caspar; Travis, Justin M J; Lens, Luc; Matthysen, Erik

2016-08-01

As biodiversity hotspots are often characterized by high human population densities, implementation of conservation management practices that focus only on the protection and enlargement of pristine habitats is potentially unrealistic. An alternative approach to curb species extinction risk involves improving connectivity among existing habitat patches. However, evaluation of spatially explicit management strategies is challenging, as predictive models must account for the process of dispersal, which is difficult in terms of both empirical data collection and modelling.Here, we use a novel, individual-based modelling platform that couples demographic and mechanistic dispersal models to evaluate the effectiveness of realistic management scenarios tailored to conserve forest birds in a highly fragmented biodiversity hotspot. Scenario performance is evaluated based on the spatial population dynamics of a well-studied forest bird species.The largest population increase was predicted to occur under scenarios increasing habitat area. However, the effectiveness was sensitive to spatial planning. Compared to adding one large patch to the habitat network, adding several small patches yielded mixed benefits: although overall population sizes increased, specific newly created patches acted as dispersal sinks, which compromised population persistence in some existing patches. Increasing matrix connectivity by the creation of stepping stones is likely to result in enhanced dispersal success and occupancy of smaller patches. Synthesis and applications . We show that the effectiveness of spatial management is strongly driven by patterns of individual dispersal across landscapes. For species conservation planning, we advocate the use of models that incorporate adequate realism in demography and, particularly, in dispersal behaviours.

Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

International Nuclear Information System (INIS)

Saraswati, Teguh Endah; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

2017-01-01

Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH 3 ). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory. (paper)

Understanding valence-shell electron-pair repulsion (VSEPR) theory using origami molecular models

Science.gov (United States)

Endah Saraswati, Teguh; Saputro, Sulistyo; Ramli, Murni; Praseptiangga, Danar; Khasanah, Nurul; Marwati, Sri

2017-01-01

Valence-shell electron-pair repulsion (VSEPR) theory is conventionally used to predict molecular geometry. However, it is difficult to explore the full implications of this theory by simply drawing chemical structures. Here, we introduce origami modelling as a more accessible approach for exploration of the VSEPR theory. Our technique is simple, readily accessible and inexpensive compared with other sophisticated methods such as computer simulation or commercial three-dimensional modelling kits. This method can be implemented in chemistry education at both the high school and university levels. We discuss the example of a simple molecular structure prediction for ammonia (NH3). Using the origami model, both molecular shape and the scientific justification can be visualized easily. This ‘hands-on’ approach to building molecules will help promote understanding of VSEPR theory.

Molecular Simulation of Adsorption in Microporous Materials

Directory of Open Access Journals (Sweden)

Yiannourakou M.

2013-11-01

Full Text Available The development of industrial software, the decreasing cost of computing time, and the availability of well-tested forcefields make molecular simulation increasingly attractive for chemical engineers. We present here several applications of Monte-Carlo simulation techniques, applied to the adsorption of fluids in microporous solids such as zeolites and model carbons (pores < 2 nm. Adsorption was computed in the Grand Canonical ensemble with the MedeA®-GIBBS software, using energy grids to decrease computing time. MedeA®-GIBBS has been used for simulations in the NVT or NPT ensembles to obtain the density and fugacities of fluid phases. Simulation results are compared with experimental pure component isotherms in zeolites (hydrocarbon gases, water, alkanes, aromatics, ethanethiol, etc., and mixtures (methane-ethane, n-hexane-benzene, over a large range of temperatures. Hexane/benzene selectivity inversions between silicalite and Na-faujasites are well predicted with published forcefields, providing an insight on the underlying mechanisms. Also, the adsorption isotherms in Na-faujasites for light gases or ethane-thiol are well described. Regarding organic adsorbents, models of mature kerogen or coal were built in agreement with known chemistry of these systems. Obtaining realistic kerogen densities with the simple relaxation approach considered here is encouraging for the investigation of other organic systems. Computing excess sorption curves in qualitative agreement with those recently measured on dry samples of gas shale is also favorable. Although still preliminary, such applications illustrate the strength of molecular modeling in understanding complex systems in conditions where experiments are difficult.

Cross-link guided molecular modeling with ROSETTA.

Directory of Open Access Journals (Sweden)

Abdullah Kahraman

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

The Effect of Realistic Mathematics Education Approach on Students' Achievement And Attitudes Towards Mathematics

Directory of Open Access Journals (Sweden)

Effandi Zakaria

2017-02-01

Full Text Available This study was conducted to determine the effect of Realistic Mathematics Education Approach on mathematics achievement and student attitudes towards mathematics. This study also sought determine the relationship between student achievement and attitudes towards mathematics. This study used a quasi-experimental design conducted on 61 high school students at SMA Unggul Sigli. Students were divided into two groups, the treatment group $(n = 30$ namely, the Realistic Mathematics Approach group (PMR and the control group $(n = 31$ namely, the traditional group. This study was conducted for six weeks. The instruments used in this study were the achievement test and the attitudes towards mathematics questionnaires. Data were analyzed using SPSS. To determine the difference in mean achievement and attitudes between the two groups, data were analyzed using one-way ANOVA test. The result showed significant differences between the Realistic Mathematics Approach and the traditional approach in terms of achievement. The study showed no significant difference between the Realistic Mathematics Approach and the traditional approach in term of attitudes towards mathematics. It can be concluded that the use of realistic mathematics education approach enhanced students' mathematics achievement, but not attitudes towards mathematics. The Realistic Mathematics Education Approach encourage students to participate actively in the teaching and learning of mathematics. Thus, Realistic Mathematics Education Approach is an appropriate methods to improve the quality of teaching and learning process.

Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

DEFF Research Database (Denmark)

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

2007-01-01

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

Molecular modeling-driven approach for identification of Janus kinase 1 inhibitors through 3D-QSAR, docking and molecular dynamics simulations.

Science.gov (United States)

Itteboina, Ramesh; Ballu, Srilata; Sivan, Sree Kanth; Manga, Vijjulatha

2017-10-01

Janus kinase 1 (JAK 1) belongs to the JAK family of intracellular nonreceptor tyrosine kinase. JAK-signal transducer and activator of transcription (JAK-STAT) pathway mediate signaling by cytokines, which control survival, proliferation and differentiation of a variety of cells. Three-dimensional quantitative structure activity relationship (3 D-QSAR), molecular docking and molecular dynamics (MD) methods was carried out on a dataset of Janus kinase 1(JAK 1) inhibitors. Ligands were constructed and docked into the active site of protein using GLIDE 5.6. Best docked poses were selected after analysis for further 3 D-QSAR analysis using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methodology. Employing 60 molecules in the training set, 3 D-QSAR models were generate that showed good statistical reliability, which is clearly observed in terms of r 2 ncv and q 2 loo values. The predictive ability of these models was determined using a test set of 25 molecules that gave acceptable predictive correlation (r 2 Pred ) values. The key amino acid residues were identified by means of molecular docking, and the stability and rationality of the derived molecular conformations were also validated by MD simulation. The good consonance between the docking results and CoMFA/CoMSIA contour maps provides helpful clues about the reasonable modification of molecules in order to design more efficient JAK 1 inhibitors. The developed models are expected to provide some directives for further synthesis of highly effective JAK 1 inhibitors.

The effects of simulating a realistic eye model on the eye dose of an adult male undergoing head computed tomography.

Science.gov (United States)

Akhlaghi, Parisa; Ebrahimi-Khankook, Atiyeh; Vejdani-Noghreiyan, Alireza

2017-05-01

In head computed tomography, radiation upon the eye lens (as an organ with high radiosensitivity) may cause lenticular opacity and cataracts. Therefore, quantitative dose assessment due to exposure of the eye lens and surrounding tissue is a matter of concern. For this purpose, an accurate eye model with realistic geometry and shape, in which different eye substructures are considered, is needed. To calculate the absorbed radiation dose of visual organs during head computed tomography scans, in this study, an existing sophisticated eye model was inserted at the related location in the head of the reference adult male phantom recommended by the International Commission on Radiological Protection (ICRP). Then absorbed doses and distributions of energy deposition in different parts of this eye model were calculated and compared with those based on a previous simple eye model. All calculations were done using the Monte Carlo code MCNP4C for tube voltages of 80, 100, 120 and 140 kVp. In spite of the similarity of total dose to the eye lens for both eye models, the dose delivered to the sensitive zone, which plays an important role in the induction of cataracts, was on average 3% higher for the sophisticated model as compared to the simple model. By increasing the tube voltage, differences between the total dose to the eye lens between the two phantoms decrease to 1%. Due to this level of agreement, use of the sophisticated eye model for patient dosimetry is not necessary. However, it still helps for an estimation of doses received by different eye substructures separately.

Moving contact lines: linking molecular dynamics and continuum-scale modelling.

Science.gov (United States)

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-04

Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

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.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

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

Multiscale Modeling of PEEK Using Reactive Molecular Dynamics Modeling and Micromechanics

Science.gov (United States)

Pisani, William A.; Radue, Matthew; Chinkanjanarot, Sorayot; Bednarcyk, Brett A.; Pineda, Evan J.; King, Julia A.; Odegard, Gregory M.

2018-01-01

Polyether ether ketone (PEEK) is a high-performance, semi-crystalline thermoplastic that is used in a wide range of engineering applications, including some structural components of aircraft. The design of new PEEK-based materials requires a precise understanding of the multiscale structure and behavior of semi-crystalline PEEK. Molecular Dynamics (MD) modeling can efficiently predict bulk-level properties of single phase polymers, and micromechanics can be used to homogenize those phases based on the overall polymer microstructure. In this study, MD modeling was used to predict the mechanical properties of the amorphous and crystalline phases of PEEK. The hierarchical microstructure of PEEK, which combines the aforementioned phases, was modeled using a multiscale modeling approach facilitated by NASA's MSGMC. The bulk mechanical properties of semi-crystalline PEEK predicted using MD modeling and MSGMC agree well with vendor data, thus validating the multiscale modeling approach.

Towards realistic string vacua from branes at singularities

Science.gov (United States)

Conlon, Joseph P.; Maharana, Anshuman; Quevedo, Fernando

2009-05-01

We report on progress towards constructing string models incorporating both realistic D-brane matter content and moduli stabilisation with dynamical low-scale supersymmetry breaking. The general framework is that of local D-brane models embedded into the LARGE volume approach to moduli stabilisation. We review quiver theories on del Pezzo n (dPn) singularities including both D3 and D7 branes. We provide supersymmetric examples with three quark/lepton families and the gauge symmetries of the Standard, Left-Right Symmetric, Pati-Salam and Trinification models, without unwanted chiral exotics. We describe how the singularity structure leads to family symmetries governing the Yukawa couplings which may give mass hierarchies among the different generations. We outline how these models can be embedded into compact Calabi-Yau compactifications with LARGE volume moduli stabilisation, and state the minimal conditions for this to be possible. We study the general structure of soft supersymmetry breaking. At the singularity all leading order contributions to the soft terms (both gravity- and anomaly-mediation) vanish. We enumerate subleading contributions and estimate their magnitude. We also describe model-independent physical implications of this scenario. These include the masses of anomalous and non-anomalous U(1)'s and the generic existence of a new hyperweak force under which leptons and/or quarks could be charged. We propose that such a gauge boson could be responsible for the ghost muon anomaly recently found at the Tevatron's CDF detector.

Agent-based modeling traction force mediated compaction of cell-populated collagen gels using physically realistic fibril mechanics.

Science.gov (United States)

Reinhardt, James W; Gooch, Keith J

2014-02-01

Agent-based modeling was used to model collagen fibrils, composed of a string of nodes serially connected by links that act as Hookean springs. Bending mechanics are implemented as torsional springs that act upon each set of three serially connected nodes as a linear function of angular deflection about the central node. These fibrils were evaluated under conditions that simulated axial extension, simple three-point bending and an end-loaded cantilever. The deformation of fibrils under axial loading varied <0.001% from the analytical solution for linearly elastic fibrils. For fibrils between 100 μm and 200 μm in length experiencing small deflections, differences between simulated deflections and their analytical solutions were <1% for fibrils experiencing three-point bending and <7% for fibrils experiencing cantilever bending. When these new rules for fibril mechanics were introduced into a model that allowed for cross-linking of fibrils to form a network and the application of cell traction force, the fibrous network underwent macroscopic compaction and aligned between cells. Further, fibril density increased between cells to a greater extent than that observed macroscopically and appeared similar to matrical tracks that have been observed experimentally in cell-populated collagen gels. This behavior is consistent with observations in previous versions of the model that did not allow for the physically realistic simulation of fibril mechanics. The significance of the torsional spring constant value was then explored to determine its impact on remodeling of the simulated fibrous network. Although a stronger torsional spring constant reduced the degree of quantitative remodeling that occurred, the inclusion of torsional springs in the model was not necessary for the model to reproduce key qualitative aspects of remodeling, indicating that the presence of Hookean springs is essential for this behavior. These results suggest that traction force mediated matrix

Generating realistic roofs over a rectilinear polygon

KAUST Repository

Ahn, Heekap; Bae, Sangwon; Knauer, Christian; Lee, Mira; Shin, Chansu; Vigneron, Antoine E.

2011-01-01

Given a simple rectilinear polygon P in the xy-plane, a roof over P is a terrain over P whose faces are supported by planes through edges of P that make a dihedral angle π/4 with the xy-plane. In this paper, we introduce realistic roofs by imposing

Realistic torso phantom for calibration of in-vivo transuranic-nuclide counting facilities

Energy Technology Data Exchange (ETDEWEB)

Shirotani, Takashi

1988-11-01

A realistic torso phantom with average body size of Japanese adult males has been developed for the calibration of counting systems used for in-vivo measurements of plutonium and other actinides. The phantom contains removable model organs (lungs, liver, kidneys and heart), model trachea and artificial rib cage, and also includes chest plates that can be placed over the chest to simulate wide range adipose/muscle ratio in the human chest. Tissue substitutes used in the phantom were made of polyurethane with different concentrations of ester of phosphoric acid. Model lungs were made of foamed polyurethane with small quantities of the additive, and the artificial rib cage was made of epoxy resin with calcium carbonate. The experimental data have shown that the phantom can be used as a standard phantom for the calibration.

Realistic Visualization of Virtual Views and Virtual Cinema

DEFF Research Database (Denmark)

Livatino, Salvatore

2005-01-01

Realistic Virtual View Visualization is a new field of research which has received increasing attention in recent years. It is strictly related to the increased popularity of virtual reality and the spread of its applications, among which virtual photography and cinematography. The use of computer...... generated characters, "virtual actors", in the motion picture production increases every day. While the most known computer graphics techniques have largely been adopted successfully in nowadays fictions, it still remains very challenging to implement virtual actors which would resemble, visually, human...... beings. Interestingly, film directors have been looking at the recent progress achieved by the research community in the field of realistic visualization of virtual views, and they have successfully implemented state of the art research approaches in their productions. An innovative concept...

Digital learning material for experimental design and model building in molecular biology

NARCIS (Netherlands)

Aegerter-Wilmsen, T.

2005-01-01

Designing experimental approaches is a major cognitive skill in molecular biology research, and building models, including quantitative ones, is a cognitive skill which is rapidly gaining importance. Since molecular biology education at university level is aimed at educating future researchers, we

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

Forcefields based molecular modeling on the mechanical and physical properties of emeraldine base polyaniline

NARCIS (Netherlands)

Chen, X.; Yuan, C.A.; Wong, K.Y.; Zhang, G.Q.

2010-01-01

Molecular dynamics (MD) and molecular mechanical (MM) analysis are carried out to provide reliable and accurate model for emeraldine base polyaniline. This study validate the forcefields and model with the physical and mechanical properties of the polyaniline. The temperature effects on non-bond

Skin dose in longitudinal and transverse linac-MRIs using Monte Carlo and realistic 3D MRI field models.

Science.gov (United States)

Keyvanloo, A; Burke, B; Warkentin, B; Tadic, T; Rathee, S; Kirkby, C; Santos, D M; Fallone, B G

2012-10-01

The magnetic fields of linac-MR systems modify the path of contaminant electrons in photon beams, which alters patient skin dose. To accurately quantify the magnitude of changes in skin dose, the authors use Monte Carlo calculations that incorporate realistic 3D magnetic field models of longitudinal and transverse linac-MR systems. Finite element method (FEM) is used to generate complete 3D magnetic field maps for 0.56 T longitudinal and transverse linac-MR magnet assemblies, as well as for representative 0.5 and 1.0 T Helmholtz MRI systems. EGSnrc simulations implementing these 3D magnetic fields are performed. The geometry for the BEAMnrc simulations incorporates the Varian 600C 6 MV linac, magnet poles, the yoke, and the magnetic shields of the linac-MRIs. Resulting phase-space files are used to calculate the central axis percent depth-doses in a water phantom and 2D skin dose distributions for 70 μm entrance and exit layers using DOSXYZnrc. For comparison, skin doses are also calculated in the absence of magnetic field, and using a 1D magnetic field with an unrealistically large fringe field. The effects of photon field size, air gap (longitudinal configuration), and angle of obliquity (transverse configuration) are also investigated. Realistic modeling of the 3D magnetic fields shows that fringe fields decay rapidly and have a very small magnitude at the linac head. As a result, longitudinal linac-MR systems mostly confine contaminant electrons that are generated in the air gap and have an insignificant effect on electrons produced further upstream. The increase in the skin dose for the longitudinal configuration compared to the zero B-field case varies from ∼1% to ∼14% for air gaps of 5-31 cm, respectively. (All dose changes are reported as a % of D(max).) The increase is also field-size dependent, ranging from ∼3% at 20 × 20 cm(2) to ∼11% at 5 × 5 cm(2). The small changes in skin dose are in contrast to significant increases that are

Analysis of Heterogeneous Networks with Dual Connectivity in a Realistic Urban Deployment

DEFF Research Database (Denmark)

Gerardino, Guillermo Andrés Pocovi; Barcos, Sonia; Wang, Hua

2015-01-01

the performance in this realistic layout. Due to the uneven load distribution observed in realistic deployments, DC is able to provide fast load balancing gains also at relatively high load - and not only at low load as typically observed in 3GPP scenarios. For the same reason, the proposed cell selection...

Molecular modeling of auxin transport inhibitors

International Nuclear Information System (INIS)

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

1990-01-01

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

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

Science.gov (United States)

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

Toluene model for molecular dynamics simulations in the ranges 298

NARCIS (Netherlands)

Fioroni, M.; Vogt, D.

2004-01-01

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

Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

Science.gov (United States)

Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

2014-01-01

Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

Energy Technology Data Exchange (ETDEWEB)

Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

2014-12-09

The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. PMID:25999313

Developing workshop module of realistic mathematics education: Follow-up workshop

Science.gov (United States)

Palupi, E. L. W.; Khabibah, S.

2018-01-01

Realistic Mathematics Education (RME) is a learning approach which fits the aim of the curriculum. The success of RME in teaching mathematics concepts, triggering students’ interest in mathematics and teaching high order thinking skills to the students will make teachers start to learn RME. Hence, RME workshop is often offered and done. This study applied development model proposed by Plomp. Based on the study by RME team, there are three kinds of RME workshop: start-up workshop, follow-up workshop, and quality boost. However, there is no standardized or validated module which is used in that workshops. This study aims to develop a module of RME follow-up workshop which is valid and can be used. Plopm’s developmental model includes materials analysis, design, realization, implementation, and evaluation. Based on the validation, the developed module is valid. While field test shows that the module can be used effectively.

Molecular modeling of polymer composite-analyte interactions in electronic nose sensors

Science.gov (United States)

Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K. S.

2003-01-01

We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL electronic nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereoisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings with no hydrogens. The Dreiding 2.21 force field is used for the polymer, solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4-vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic and organic compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites. c2003 Elsevier Science B.V. All rights reserved.

Molecular modeling in the development of metal radiopharmaceuticals

International Nuclear Information System (INIS)

Green, M.A.

1993-10-01

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

Quantum molecular dynamics study of the Su-Schrieffer-Heeger model

NARCIS (Netherlands)

Michielsen, Kristel; Raedt, Hans De

A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to

Molecular Modeling of Interfacial Behaviors of Nanomaterials

Science.gov (United States)

2007-05-01

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

Robust control of decoherence in realistic one-qubit quantum gates

International Nuclear Information System (INIS)

Protopopescu, V; Perez, R; D'Helon, C; Schmulen, J

2003-01-01

We present an open-loop (bang-bang) scheme to control decoherence in a generic one-qubit quantum gate and implement it in a realistic simulation. The system is consistently described within the spin-boson model, with interactions accounting for both adiabatic and thermal decoherence. The external control is included from the beginning in the Hamiltonian as an independent interaction term. After tracing out the environment modes, reduced equations are obtained for the two-level system in which the effects of both decoherence and external control appear explicitly. The controls are determined exactly from the condition to eliminate decoherence, i.e. to restore unitarity. Numerical simulations show excellent performance and robustness of the proposed control scheme

Model-based dose calculations for COMS eye plaque brachytherapy using an anatomically realistic eye phantom.

Science.gov (United States)

Lesperance, Marielle; Inglis-Whalen, M; Thomson, R M

2014-02-01

To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with(125)I, (103)Pd, or (131)Cs seeds, and to investigate doses to ocular structures. An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20-30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%-10% and 13%-14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%-17% and 29%-34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up to 16%. In the full eye model

Model-based dose calculations for COMS eye plaque brachytherapy using an anatomically realistic eye phantom

International Nuclear Information System (INIS)

Lesperance, Marielle; Inglis-Whalen, M.; Thomson, R. M.

2014-01-01

Purpose : To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with 125 I, 103 Pd, or 131 Cs seeds, and to investigate doses to ocular structures. Methods : An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Results : Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up

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

Indian Academy of Sciences (India)

Wintec

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

Modeling individual movement decisions of brown hare (Lepus europaeus) as a key concept for realistic spatial behavior and exposure: A population model for landscape-level risk assessment.

Science.gov (United States)

Kleinmann, Joachim U; Wang, Magnus

2017-09-01

Spatial behavior is of crucial importance for the risk assessment of pesticides and for the assessment of effects of agricultural practice or multiple stressors, because it determines field use, exposition, and recovery. Recently, population models have increasingly been used to understand the mechanisms driving risk and recovery or to conduct landscape-level risk assessments. To include spatial behavior appropriately in population models for use in risk assessments, a new method, "probabilistic walk," was developed, which simulates the detailed daily movement of individuals by taking into account food resources, vegetation cover, and the presence of conspecifics. At each movement step, animals decide where to move next based on probabilities being determined from this information. The model was parameterized to simulate populations of brown hares (Lepus europaeus). A detailed validation of the model demonstrated that it can realistically reproduce various natural patterns of brown hare ecology and behavior. Simulated proportions of time animals spent in fields (PT values) were also comparable to field observations. It is shown that these important parameters for the risk assessment may, however, vary in different landscapes. The results demonstrate the value of using population models to reduce uncertainties in risk assessment and to better understand which factors determine risk in a landscape context. Environ Toxicol Chem 2017;36:2299-2307. © 2017 SETAC. © 2017 SETAC.

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.

Application of realistic (best- estimate) methodologies for large break loss of coolant (LOCA) safety analysis: licensing of Westinghouse ASTRUM evaluation model in Spain

International Nuclear Information System (INIS)

Lage, Carlos; Frepoli, Cesare

2010-01-01

When the LOCA Final Acceptance Criteria for Light Water Reactors was issued in Appendix K of 10CFR50 both the USNRC and the industry recognized that the rule was highly conservative. At that time, however, the degree of conservatism in the analysis could not be quantified. As a result, the USNRC began a research program to identify the degree of conservatism in those models permitted in the Appendix K rule and to develop improved thermal-hydraulic computer codes so that realistic accident analysis calculations could be performed. The overall results of this research program quantified the conservatism in the Appendix K rule and confirmed that some relaxation of the rule can be made without a loss in safety to the public. Also, from a risk-informed perspective it is recognized that conservatism is not always a complete defense for lack of sophistication in models. In 1988, as a result of the improved understanding of LOCA phenomena, the USNRC staff amended the requirements of 10 CFR 50.46 and Appendix K, 'ECCS Evaluation Models', so that a realistic evaluation model may be used to analyze the performance of the ECCS during a hypothetical LOCA. Under the amended rules, best-estimate plus uncertainty (BEPU) thermal-hydraulic analysis may be used in place of the overly prescriptive set of models mandated by Appendix K rule. Further guidance for the use of best-estimate codes was provided in Regulatory Guide 1.157 To demonstrate use of the revised ECCS rule, the USNRC and its consultants developed a method called the Code Scaling, Applicability, and Uncertainty (CSAU) evaluation methodology as an approach for defining and qualifying a best-estimate thermal-hydraulic code and quantifying the uncertainties in a LOCA analysis. More recently the CSAU principles have been generalized in the Evaluation Model Development and Assessment Process (EMDAP) of Regulatory Guide 1.203. ASTRUM is the Westinghouse Best Estimate Large Break LOCA evaluation model applicable to two-, three

Application of Molecular Modeling to Urokinase Inhibitors Development

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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.

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

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Karademir Andersson, Ahu; Cohn, Marita

2017-03-01

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

Molecular Models for DSMC Simulations of Metal Vapor Deposition

OpenAIRE

Venkattraman, A; Alexeenko, Alina A

2010-01-01

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

Realistic Affective Forecasting: The Role of Personality

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Hoerger, Michael; Chapman, Ben; Duberstein, Paul

2016-01-01

Affective forecasting often drives decision making. Although affective forecasting research has often focused on identifying sources of error at the event level, the present investigation draws upon the ‘realistic paradigm’ in seeking to identify factors that similarly influence predicted and actual emotions, explaining their concordance across individuals. We hypothesized that the personality traits neuroticism and extraversion would account for variation in both predicted and actual emotional reactions to a wide array of stimuli and events (football games, an election, Valentine’s Day, birthdays, happy/sad film clips, and an intrusive interview). As hypothesized, individuals who were more introverted and neurotic anticipated, correctly, that they would experience relatively more unpleasant emotional reactions, and those who were more extraverted and less neurotic anticipated, correctly, that they would experience relatively more pleasant emotional reactions. Personality explained 30% of the concordance between predicted and actual emotional reactions. Findings suggest three purported personality processes implicated in affective forecasting, highlight the importance of individual-differences research in this domain, and call for more research on realistic affective forecasts. PMID:26212463

Using technology to engage hospitalised patients in their care: a realist review.

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Roberts, Shelley; Chaboyer, Wendy; Gonzalez, Ruben; Marshall, Andrea

2017-06-06

Patient participation in health care is associated with improved outcomes for patients and hospitals. New technologies are creating vast potential for patients to participate in care at the bedside. Several studies have explored patient use, satisfaction and perceptions of health information technology (HIT) interventions in hospital. Understanding what works for whom, under what conditions, is important when considering interventions successfully engaging patients in care. This realist review aimed to determine key features of interventions using bedside technology to engage hospital patients in their care and analyse these in terms of context, mechanisms and outcomes. A realist review was chosen to explain how and why complex HIT interventions work or fail within certain contexts. The review was guided by Pawson's realist review methodology, involving: clarifying review scope; searching for evidence; data extraction and evidence appraisal; synthesising evidence and drawing conclusions. Author experience and an initial literature scope provided insight and review questions and theories (propositions) around why interventions worked were developed and iteratively refined. A purposive search was conducted to find evidence to support, refute or identify further propositions, which formed an explanatory model. Each study was 'mined' for evidence to further develop the propositions and model. Interactive learning was the overarching theme of studies using technology to engage patients in their care. Several propositions underpinned this, which were labelled: information sharing; self-assessment and feedback; tailored education; user-centred design; and support in use of HIT. As studies were mostly feasibility or usability studies, they reported patient-centred outcomes including patient acceptability, satisfaction and actual use of HIT interventions. For each proposition, outcomes were proposed to come about by mechanisms including improved communication, shared

Global Paleobathymetry Reconstruction with Realistic Shelf-Slope and Sediment Wedge

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Goswami, A.; Hinnov, L. A.; Gnanadesikan, A.; Olson, P.

2013-12-01

We present paleo-ocean bathymetry reconstructions in a 0.1°x0.1° resolution, using simple geophysical models (Plate Model Equation for oceanic lithosphere), published ages of the ocean floor (Müller et al. 2008), and modern world sediment thickness data (Divins 2003). The motivation is to create realistic paleobathymetry to understand the effect of ocean floor roughness on tides and heat transport in paleoclimate simulations. The values for the parameters in the Plate Model Equation are deduced from Crosby et al. (2006) and are used together with ocean floor age to model Depth to Basement. On top of the Depth to Basement, we added an isostatically adjusted multilayer sediment layer, as indicated from sediment thickness data of the modern oceans and marginal seas (Divins 2003). We also created another version of the sediment layer from the Müller et al. dataset. The Depth to Basement with the appropriate sediment layer together represent a realistic paleobathymetry. A Sediment Wedge was modeled to complement the reconstructed paleobathymetry by extending it to the coastlines. In this process we added a modeled Continental Shelf and Continental Slope to match the extent of the reconstructed paleobathymetry. The Sediment Wedge was prepared by studying the modern ocean where a complete history of seafloor spreading is preserved (north, south and central Atlantic Ocean, Southern Ocean between Australia-Antarctica, and the Pacific Ocean off the west coast of South America). The model takes into account the modern continental shelf-slope structure (as evident from ETOPO1/ETOPO5), tectonic margin type (active vs. passive margin) and age of the latest tectonic activity (USGS & CGMW). Once the complete ocean bathymetry is modeled, we combine it with PALEOMAP (Scotese, 2011) continental reconstructions to produce global paleoworld elevation-bathymetry maps. Modern time (00 Ma) was assumed as a test case. Using the above-described methodology we reconstructed modern ocean

On the molecular mechanism of surface charge amplification and related phenomena at aqueous polyelectrolyte-graphene interfaces

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J.M. Simonson

2011-09-01

Full Text Available In this communication we illustrate the occurrence of a recently reported new phenomenon of surface-charge amplification, SCA, (originally dubbed overcharging, OC, [Jimenez-Angeles F. and Lozada-Cassou M., J. Phys. Chem. B, 2004, 108, 7286] by means of molecular dynamics simulation of aqueous electrolytes solutions involving multivalent cations in contact with charged graphene walls and the presence of short-chain lithium polystyrene sulfonates where the solvent water is described explicitly with a realistic molecular model. We show that the occurrence of SCA in these systems, in contrast to that observed in primitive models, involves neither contact co-adsorption of the negatively charged macroions nor divalent cations with a large size and charge asymmetry as required in the case of implicit solvents. In fact the SCA phenomenon hinges around the preferential adsorption of water (over the hydrated ions with an average dipolar orientation such that the charges of the water's hydrogen and oxygen sites induce magnification rather than screening of the positive-charged graphene surface, within a limited range of surface-charge density.

Beyond the realist turn: a socio-material analysis of heart failure self-care.

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McDougall, Allan; Kinsella, Elizabeth Anne; Goldszmidt, Mark; Harkness, Karen; Strachan, Patricia; Lingard, Lorelei

2018-01-01

For patients living with chronic illnesses, self-care has been linked with positive outcomes such as decreased hospitalisation, longer lifespan, and improved quality of life. However, despite calls for more and better self-care interventions, behaviour change trials have repeatedly fallen short on demonstrating effectiveness. The literature on heart failure (HF) stands as a case in point, and a growing body of HF studies advocate realist approaches to self-care research and policymaking. We label this trend the 'realist turn' in HF self-care. Realist evaluation and realist interventions emphasise that the relationship between self-care interventions and positive health outcomes is not fixed, but contingent on social context. This paper argues socio-materiality offers a productive framework to expand on the idea of social context in realist accounts of HF self-care. This study draws on 10 interviews as well as researcher reflections from a larger study exploring health care teams for patients with advanced HF. Leveraging insights from actor-network theory (ANT), this study provides two rich narratives about the contextual factors that influence HF self-care. These descriptions portray not self-care contexts but self-care assemblages, which we discuss in light of socio-materiality. © 2018 Foundation for the Sociology of Health & Illness.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

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

2017-09-01

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

Adsorption of molecular hydrogen on nanostructered surfaces

International Nuclear Information System (INIS)

Uranga Piña, Llinersy; Martínez Mesa, Aliezer; Seifert, Gotthard

2015-01-01

Were investigated the effect of the structural characteristics of model nanoporous environments on the adsorption of molecular hydrogen. The adsorption properties of the target nanostructures (graphene and ZnO sheets, carbon foams, metal-organic frameworks) are evaluated in a broad range of thermodynamic conditions. The study is carried out within the density functional theory for quantum fluids at finite temperature (QLDFT), which allows to account for the many-body and quantum delocalization effects in a single theoretical framework. The exchange-correlation (excess) functional is derived from the empirical equation of state of the homogeneous system. We focus on the evaluation of hydrogen storage capacities of the substrates and on the emergence of quantum effects triggered by the confinement imposed by the host structure. The approach provides accurate estimates of the hydrogen storage capacities for realistic adsorptive media. The relation between the microscopic structure of the hydrogen fluid and the calculated adsorption properties is also addressed. (full text)

Molecular Mechanism of Gastric Carcinogenesis in Helicobacter pylori-Infected Rodent Models

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Takeshi Toyoda

2014-06-01