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Continuum, Discrete, and Explicit Solvation Models for Describing the Low-Lying Absorption Spectrum of the Pterin Acid in Aqueous Environment

Jaramillo Garcia, Paula Andrea; Coutinho, Kaline Rabelo; Canuto, Sylvio Roberto Accioly
Fonte: JOHN WILEY & SONS INC Publicador: JOHN WILEY & SONS INC
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
45.92%
The absorption spectrum of the acid form of pterin in water was investigated theoretically. Different procedures using continuum, discrete, and explicit models were used to include the solvation effect on the absorption spectrum, characterized by two bands. The discrete and explicit models used Monte Carlo simulation to generate the liquid structure and time-dependent density functional theory (B3LYP/6-31G+(d)) to obtain the excitation energies. The discrete model failed to give the correct qualitative effect on the second absorption band. The continuum model, in turn, has given a correct qualitative picture and a semiquantitative description. The explicit use of 29 solvent molecules, forming a hydration shell of 6 angstrom, embedded in the electrostatic field of the remaining solvent molecules, gives absorption transitions at 3.67 and 4.59 eV in excellent agreement with the S(0)-S(1) and S(0)-S(2) absorption bands at of 3.66 and 4.59 eV, respectively, that characterize the experimental spectrum of pterin in water environment. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110: 2371-2377, 2010

Fluid dynamics of air in a packed bed: velocity profiles and the continuum model assumption

NEGRINI, A. L.; FUELBER, A.; FREIRE, J. T.; THOMÉO, J. C.
Fonte: Brazilian Society of Chemical Engineering Publicador: Brazilian Society of Chemical Engineering
Tipo: Artigo de Revista Científica Formato: 421-432
ENG
Relevância na Pesquisa
55.87%
Air flow through packed beds was analyzed experimentally under conditions ranging from those that reinforce the effect of the wall on the void fraction to those that minimize it. The packing was spherical particles, with a tube-to-particle diameter ratio (D/dp) between 3 and 60. Air flow rates were maintained between 1.3 and 4.44 m3/min, and gas velocity was measured with a Pitot tube positioned above the bed exit. Measurements were made at various radial and angular coordinate values, allowing the distribution of air flow across the bed to be described in detail. Comparison of the experimentally observed radial profiles with those derived from published equations revealed that at high D/dp ratios the measured and calculated velocity profiles behaved similarly. At low ratios, oscillations in the velocity profiles agreed with those in the voidage profiles, signifying that treating the porous medium as a continuum medium is questionable in these cases.

Fluid dynamics of air in a packed bed: velocity profiles and the continuum model assumption

NEGRINI,A. L.; FUELBER,A.; FREIRE,J. T.; THOMÉO,J. C.
Fonte: Brazilian Society of Chemical Engineering Publicador: Brazilian Society of Chemical Engineering
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/1999 EN
Relevância na Pesquisa
55.87%
Air flow through packed beds was analyzed experimentally under conditions ranging from those that reinforce the effect of the wall on the void fraction to those that minimize it. The packing was spherical particles, with a tube-to-particle diameter ratio (D/dp) between 3 and 60. Air flow rates were maintained between 1.3 and 4.44 m3/min, and gas velocity was measured with a Pitot tube positioned above the bed exit. Measurements were made at various radial and angular coordinate values, allowing the distribution of air flow across the bed to be described in detail. Comparison of the experimentally observed radial profiles with those derived from published equations revealed that at high D/dp ratios the measured and calculated velocity profiles behaved similarly. At low ratios, oscillations in the velocity profiles agreed with those in the voidage profiles, signifying that treating the porous medium as a continuum medium is questionable in these cases.

Molecular surface-free continuum model for electrodiffusion processes

Lu, Benzhuo; McCammon, J. Andrew
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 21/01/2008 EN
Relevância na Pesquisa
45.93%
Incorporation of van der Waals interactions enables the continuum model of electrodiffusion in biomolecular system to avoid the artifacts of introducing a molecular surface and the painful task of the surface mesh generation. Calculation examples show that the electrostatics, diffusion-reaction kinetics, and molecular surface defined as an isosurface of a certain density distribution can be extracted from the solution of the Poisson-Nernst-Planck equations using this model. The molecular surface-free model enables a wider usage of some modern numerical methodologies such as finite element methods for biomolecular modeling, and sheds light on a new paradigm of continuum modeling for biomolecular systems.

Comparing a discrete and continuum model of the intestinal crypt

Murray, Philip J.; Walter, Alex; Fletcher, Alex G.; Edwards, Carina M.; Tindall, Marcus J.; Maini, Philip K.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.99%
The integration of processes at different scales is a key problem in the modelling of cell populations. Owing to increased computational resources and the accumulation of data at the cellular and subcellular scales, the use of discrete, cell-level models, which are typically solved using numerical simulations, has become prominent. One of the merits of this approach is that important biological factors, such as cell heterogeneity and noise, can be easily incorporated. However, it can be difficult to efficiently draw generalisations from the simulation results, as, often, many simulation runs are required to investigate model behaviour in typically large parameter spaces. In some cases, discrete cell-level models can be coarse-grained, yielding continuum models whose analysis can lead to the development of insight into the underlying simulations. In this paper we apply such an approach to the case of a discrete model of cell dynamics in the intestinal crypt. An analysis of the resulting continuum model demonstrates that there is a limited region of parameter space within which steady-state (and hence biologically realistic) solutions exist. Continuum model predictions show good agreement with corresponding results from the underlying simulations and experimental data taken from murine intestinal crypts.

A Coupled Discrete/Continuum Model for Describing Cancer-Therapeutic Transport in the Lung

Erbertseder, Karin; Reichold, Johannes; Flemisch, Bernd; Jenny, Patrick; Helmig, Rainer
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 12/03/2012 EN
Relevância na Pesquisa
46.04%
We propose a computational simulation framework for describing cancer-therapeutic transport in the lung. A discrete vascular graph model (VGM) is coupled to a double-continuum model (DCM) to determine the amount of administered therapeutic agent that will reach the cancer cells. An alveolar cell carcinoma is considered. The processes in the bigger blood vessels (arteries, arterioles, venules and veins) are described by the VGM. The processes in the alveolar capillaries and the surrounding tissue are represented by a continuum approach for porous media. The system of equations of the coupled discrete/continuum model contains terms that account for degradation processes of the therapeutic agent, the reduction of the number of drug molecules by the lymphatic system and the interaction of the drug with the tissue cells. The functionality of the coupled discrete/continuum model is demonstrated in example simulations using simplified pulmonary vascular networks, which are designed to show-off the capabilities of the model rather than being physiologically accurate.

Coupled Particulate and Continuum Model for Nanoparticle Targeted Delivery

Tan, Jifu; Wang, Shunqiang; Yang, Jie; Liu, Yaling
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
45.97%
Prediction of nanoparticle (NP) distribution in a vasculature involves transport phenomena at various scales and is crucial for the evaluation of NP delivery efficiency. A combined particulate and continuum model is developed to model NP transport and delivery processes. In the particulate model ligand-receptor binding kinetics is coupled with Brownian dynamics to study NP binding on a microscale. An analytical formula is derived to link molecular level binding parameters to particulate level adhesion and detachment rates. The obtained NP adhesion rates are then coupled with a convection-diffusion-reaction model to study NP transport and delivery at macroscale. The binding results of the continuum model agree well with those from the particulate model. The effects of shear rate, particle size and vascular geometry on NP adhesion are investigated. Attachment rates predicted by the analytical formula also agree reasonably well with the experimental data reported in literature. The developed coupled model that links ligand-receptor binding dynamics to NP adhesion rate along with macroscale transport and delivery processes may serve as a faster evaluation and prediction tool to determine NP distribution in complex vascular networks.

Continuum model of tendon pathology – where are we now?

McCreesh, Karen; Lewis, Jeremy
Fonte: Blackwell Publishing Ltd Publicador: Blackwell Publishing Ltd
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.01%
Chronic tendon pathology is a common and often disabling condition, the causes of which remain poorly understood. The continuum model of tendon pathology was proposed to provide a model for the staging of tendon pathology and to assist clinicians in managing this often complex condition (Br. J. Sports Med., 43, 2009, 409). The model presents clinical, histological and imaging evidence for the progression of tendon pathology as a three-stage continuum: reactive tendinopathy, tendon disrepair and degenerative tendinopathy. It also provides clinical information to assist in identifying the stage of pathology, in addition to proposed treatment approaches for each stage. The usefulness of such a model is determined by its ability to incorporate and inform new and emerging research. This review examines the degree to which recent research supports or refutes the continuum model and proposes future directions for clinical and research application of the model.

Applications of fractured continuum model to enhanced geothermal system heat extraction problems

Kalinina, Elena A; Klise, Katherine A; McKenna, Sean A; Hadgu, Teklu; Lowry, Thomas S
Fonte: Springer International Publishing Publicador: Springer International Publishing
Tipo: Artigo de Revista Científica
Publicado em 24/02/2014 EN
Relevância na Pesquisa
45.98%
This paper describes the applications of the fractured continuum model to the different enhanced geothermal systems reservoir conditions. The capability of the fractured continuum model to generate fracture characteristics expected in enhanced geothermal systems reservoir environments are demonstrated for single and multiple sets of fractures. Fracture characteristics are defined by fracture strike, dip, spacing, and aperture. The paper demonstrates how the fractured continuum model can be extended to represent continuous fractured features, such as long fractures, and the conditions in which the fracture density varies within the different depth intervals. Simulations of heat transport using different fracture settings were compared with regard to their heat extraction effectiveness. The best heat extraction was obtained in the case when fractures were horizontal. A conventional heat extraction scheme with vertical wells was compared to an alternative scheme with horizontal wells. The heat extraction with the horizontal wells was significantly better than with the vertical wells when the injector was at the bottom.

A continuum model for needlepunched nonwoven fabrics; Continuum model for needle punched non woven fabrics

Jearanaisilawong, Petch, 1979-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 166 p.
ENG
Relevância na Pesquisa
46.02%
Nonwoven fabrics are sheet structures created by bonding or interlocking a web (network) of fibers through mechanical, thermal or chemical processes. In general, the mechanical response of nonwoven fabrics exhibits two major characteristics. First, the mechanical response can vary significantly when the fabric is loaded along different directions, depending on the existence of a preferential orientation in the fiber arrangement and/or in the pattern of inter-fiber bonding/entanglement. Second, the mechanisms of deformation include elastic and inelastic components, accompanied by an irrecoverable evolution of the texture of the fiber network. In this work, we propose a three-dimensional, large strain continuum model for the constitutive behavior of nonwoven fabrics that accounts for the fiber network characteristics responsible for its anisotropic behavior, and captures the effects of deformation mechanisms at the micro-scale (fiber and bonds/entanglement) level. The model consists of two constitutive components: a nonlinear elastic component representing the resistances to recoverable deformation mechanisms, and a non-linear inelastic component representing the resistances to irrecoverable deformation and texture evolution. For nonwoven fabrics in which the anisotropy of fiber orientation is combined with random entanglement processes...

Dynamic renormalization group study of a generalized continuum model of crystalline surfaces

Cuerno, Rodolfo; Moro, Esteban
Fonte: The American Physical Society Publicador: The American Physical Society
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em /01/2002 ENG
Relevância na Pesquisa
45.94%
We apply the Nozières-Gallet dynamic renormalization group (RG) scheme to a continuum equilibrium model of a d-dimensional surface relaxing by linear surface tension and linear surface diffusion, and which is subject to a lattice potential favoring discrete values of the height variable. The model thus interpolates between the overdamped sine-Gordon model and a related continuum model of crystalline tensionless surfaces. The RG flow predicts the existence of an equilibrium roughening transition only for d=2 dimensional surfaces, between a flat low-temperature phase and a rough high-temperature phase in the Edwards-Wilkinson (EW) universality class. The surface is always in the flat phase for any other substrate dimensions d>2. For any value of d, the linear surface diffusion mechanism is an irrelevant perturbation of the linear surface tension mechanism, but may induce long crossovers within which the scaling properties of the linear molecular-beam epitaxy equation are observed, thus increasing the value of the sine-Gordon roughening temperature. This phenomenon originates in the nonlinear lattice potential, and is seen to occur even in the absence of a bare surface tension term. An important consequence of this is that a crystalline tensionless surface is asymptotically described at high temperatures by the EW universality class.; E. M. aknowledges the EU Grant No. HPMF-CT-2000-0487. This research has been supported by EPSRC (UK) Grant No. GR/M04426...

Including nonequilibrium interface kinetics in a continuum model for melting nanoscaled particles

Back, Julian M.; McCue, Scott W.; Moroney, Timothy J.
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em 17/11/2014 EN
Relevância na Pesquisa
45.93%
The melting temperature of a nanoscaled particle is known to decrease as the curvature of the solid-melt interface increases. This relationship is most often modelled by a Gibbs–Thomson law, with the decrease in melting temperature proposed to be a product of the curvature of the solid-melt interface and the surface tension. Such a law must break down for sufficiently small particles, since the curvature becomes singular in the limit that the particle radius vanishes. Furthermore, the use of this law as a boundary condition for a Stefan-type continuum model is problematic because it leads to a physically unrealistic form of mathematical blow-up at a finite particle radius. By numerical simulation, we show that the inclusion of nonequilibrium interface kinetics in the Gibbs–Thomson law regularises the continuum model, so that the mathematical blow up is suppressed. As a result, the solution continues until complete melting, and the corresponding melting temperature remains finite for all time. The results of the adjusted model are consistent with experimental findings of abrupt melting of nanoscaled particles. This small-particle regime appears to be closely related to the problem of melting a superheated particle.

DFT and TD-DFT investigation of IR and UV spectra of solvated molecules: comparison of two SCRF continuum models

Preat, Julien; Loos, Pierre-Francois; Assfeld, Xavier; Jacquemin, Denis; Perpete, Eric A
Fonte: John Wiley & Sons Inc Publicador: John Wiley & Sons Inc
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
45.96%
We report the calculation of liquid-phase infrared (IR) and ultraviolet (UV) spectra in the framework of the solute's response to the reaction field of several solvents. In particular, we compare these two properties for the multipolar expansion model dev

Continuum model of tendon pathology: Where are we now?

McCreesh, Karen; Lewis, Jeremy
Fonte: Wiley Publicador: Wiley
Tipo: info:eu-repo/semantics/article; all_ul_research; ul_published_reviewed
ENG
Relevância na Pesquisa
56.04%
peer-reviewed; Chronic tendon pathology is a common, and often disabling condition, the causes of which remain poorly understood. The continuum model of tendon pathology was proposed in order to provide a model for the staging of tendon pathology, and to assist clinicians in managing this often complex condition (Cook and Purdam 2009). The model presents clinical, histological and imaging evidence for the progression of tendon pathology as a three-stage continuum: reactive tendinopathy, tendon disrepair, and degenerative tendinopathy. It also provides clinical information to assist in identifying the stage of pathology, in addition to proposed treatment approaches for each stage. The usefulness of such a model is determined by its ability to incorporate and inform new and emerging research. This review examines the degree to which recent research supports or refutes the continuum model, and proposes future directions for clinical and research application of the model.; ACCEPTED; peer-reviewed

High strain rate constitutive modeling forhistorical structures subjected to blast loading

Rafsanjani, Seyedebrahim Hashemi
Fonte: Universidade do Minho Publicador: Universidade do Minho
Tipo: Tese de Doutorado
Publicado em 07/05/2015 ENG
Relevância na Pesquisa
45.98%
Doctoral Thesis Civil Engineering; The work presented here was accomplished at the Department of Civil Engineering of University of Minho. This work involves detailed numerical studies intended to better understand the blast response of masonry structures, develops strain dependent constitutive material plasticity model for masonry, and addresses iso-damage curves for typical masonry infill walls in Portugal under blast with different loading conditions, which can be adopted for practical use in the case of enclosures. A bomb explosion near a building, in addition to a great deal of casualties and losses, can cause serious effects on the building itself, such as noticeable damage on internal and external frames, collapsing walls or shutting down of critical life safety systems. Until Oklahoma City bombing in 1995, studies dealing with the blast behavior of structures were a field of limited interest in the civil engineering community. After this terrorist attack, a great deal of effort has been done to better understand the blast response of the structures and devise solutions to reduce destructive damages and casualties due to such devastative loads. Moreover, the studies on the influence of the high strain rate on mechanical characteristics of construction materials such as steel and concrete have been carried out intensively. Unfortunately...

Study of Lattice Correlation Functions at Small Times using the QCD Sum Rules Continuum Model

Allton, Chris; Capitani, Stefano
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 03/12/1997
Relevância na Pesquisa
46.07%
In this paper we study the work of Leinweber by applying the Continuum Model of QCD Sum Rules (QCDSR) to the analysis of (quenched) lattice correlation functions. We expand upon his work in several areas: we study meson states as well as baryons; we analyse data from several lattice spacings; and we include data from the Sheikholeslami-Wohlert (clover) improved action. We find that the QCDSR Continuum Model Ansatz can reproduce the data, but only for non-physical values of its parameters. This leads us to reject it as a model for hadronic correlation functions. We study the non-relativistic quark model and conclude that it predicts essentially the same form for the correlation function as the QCDSR Continuum Model approach. Furthermore, because it doesn't have the Continuum Model's restrictions on the parameters, the non-relativistic quark model can be viewed as a successful Ansatz. As well as studying the validity or otherwise of the QCDSR Continuum Model approach, this paper defines 4-parameter fitting functions that can be used to fit lattice data even for a time window close to the source. These functions are shown to be an improvement over 2-exponential fits especially in the case of mesons. We encourage the application of this approach to situations where the conventional fitting procedures are problematic due to poor ground state dominance.; Comment: 33 pages...

A continuum model for dislocation dynamics in three dimensions using the dislocation density potential functions and its application in understanding the micro-pillar size effect

Zhu, Yichao; Xiang, Yang
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
45.93%
In this paper, we present a dislocation-density-based three-dimensional continuum model, where the dislocation substructures are represented by pairs of dislocation density potential functions (DDPFs), denoted by $\phi$ and $\psi$. The slip plane distribution is characterized by the contour surfaces of $\psi$, while the distribution of dislocation curves on each slip plane is identified by the contour curves of $\phi$ which represents the plastic slip on the slip plane. By using DDPFs, we can explicitly write down an evolution equation system, which is shown consistent with the underlying discrete dislocation dynamics. The system includes i) A constitutive stress rule, which describes how the total stress field is determined in the presence of dislocation networks and applied loads; ii) A plastic flow rule, which describes how dislocation ensembles evolve. The proposed continuum model is validated through comparisons with discrete dislocation dynamics simulation results and experimental data. As an application of the proposed model, the "smaller-being-stronger" size effect observed in single-crystal micro-pillars is studied. A scaling law for the pillar flow stress $\sigma_{\text{flow}}$ against its (non-dimensionalized) size $D$ is derived to be $\sigma_{\text{flow}}\sim\log(D)/D$.

Dynamic renormalization group study of a generalized continuum model of crystalline surfaces

Cuerno, Rodolfo; Moro, Esteban
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 25/10/2001
Relevância na Pesquisa
45.94%
We apply the Nozieres-Gallet dynamic renormalization group (RG) scheme to a continuum equilibrium model of a d-dimensional surface relaxing by linear surface tension and linear surface diffusion, and which is subject to a lattice potential favoring discrete values of the height variable. The model thus interpolates between the overdamped sine-Gordon model and a related continuum model of crystalline tensionless surfaces. The RG flow predicts the existence of an equilibrium roughening transition only for d = 2 dimensional surfaces, between a flat low-temperature phase and a rough high-temperature phase in the Edwards-Wilkinson (EW) universality class. The surface is always in the flat phase for any other substrate dimensions d > 2. For any value of d, the linear surface diffusion mechanism is an irrelevant perturbation of the linear surface tension mechanism, but may induce long crossovers within which the scaling properties of the linear molecular-beam epitaxy equation are observed, thus increasing the value of the sine-Gordon roughening temperature. This phenomenon originates in the non-linear lattice potential, and is seen to occur even in the absence of a bare surface tension term. An important consequence of this is that a crystalline tensionless surface is asymptotically described at high temperatures by the EW universality class.; Comment: 22 pages...

Continuum model description of thin film growth morphology

Mou, Chung-Yu; Hsu, J. W. P.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/05/1997
Relevância na Pesquisa
45.93%
We examine the applicability of the continuum model to describe the surface morphology of a hetero-growth system: compositionally-graded, relaxed GeSi films on (001) Si substrates. Surface roughness versus lateral dimension was analyzed for samples what were grown under different conditions. We find that all samples belong to the same growth class, in which the surface roughness scales linearly with lateral size at small scales and appears to saturate at large scales. For length scales ranging from 1 nm to 100 $\mu$m, the scaling behavior can be described by a linear continuum model consisting of a surface diffusion term and a Laplacian term. However, in-depth analysis on non-universal amplitudes indicates the breaking of up-down symmetry, suggesting the presence of non-linear terms in the microscopic model. We argue that the leading non-linear term has the form of $\lambda _1(\nabla h)^2$, but its effect on scaling exponents will not be evident for length scales less than 1 mm. Therefore, the growth dynamics of this system is described by the Kuramoto-Sivashinsky equation, consisting of the two linear terms plus $\lambda _1(\nabla h)^2$, driven by a Gaussian noise. We also discuss the negative coefficient in the Laplacian term as an instability mechanism responsible for large scale film morphology on the final surface.; Comment: 25 pages...

Beyond fragmentation: the continuum model for fauna research and conservation in human-modified landscapes

Fischer, Joern; Lindenmayer, David
Fonte: Munksgaard International Publishers Publicador: Munksgaard International Publishers
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.12%
Animal distribution patterns in human-modified landscapes are often examined from the basis of the "fragmentation model", which recognises habitat patches located within an inhospitable matrix. The fragmentation model can establish correlations between landscape pattern and animal distribution patterns. However, it is limited in its ability to generate a process-based understanding of species distribution patterns. Here we propose a process-based conceptual landscape model. The "continuum model" is derived from continuum theory, and recognises the importance of space-related ecological variables alongside other factors, such as the availability of suitable food, shelter, and climatic conditions. The continuum model allows for gradual changes in these variables through space, and assumes species respond individualistically to their environment. We contrast the continuum model with the fragmentation model, and outline how it can be used to interpret and design empirical studies. While the fragmentation model may provide a satisfactory description of ecological patterns where many species are confined to human-defined "patches", the continuum model can help to establish links between fundamental ecological processes and individualistic species distribution patterns. Conservation guidelines arising from the fragmentation model will emphasise the importance of large and well-connected pre-defined "habitat" patches. Conversely...