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- Cambridge University Press
- Biblioteca Digital da Unicamp
- Universidade do Minho
- Biophysical Society
- The Biophysical Society
- American Institute of Physics
- Massachusetts Institute of Technology
- Universidade Rice
- Institute of Electrical and Electronics Engineers (IEEE Inc)
- Universidade Cornell
- Rockefeller University Press
- Rochester Instituto de Tecnologia
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## ‣ Dynamic modeling and simulation of a flexible robotic manipulator

Fonte: Cambridge University Press
Publicador: Cambridge University Press

Tipo: Artigo de Revista Científica
Formato: 523-528

Português

Relevância na Pesquisa
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#advanced manufacturing technologies#robotics#flexible robotic manipulator#dynamic modeling and simulation#vibration active control

This work focuses on the dynamic modeling of a flexible robotic manipulator with two flexible links and two revolute joints, which rotates in the horizontal plane. The dynamic equations are derived using the Newton-Euler formulation and the finite element method, based on elementary beam theory. Computer simulation results are presented to illustrate this study. The dynamic model becomes necessary for use in future design and control applications.

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## ‣ Aspects of the discretized peridynamic theory and the finite element method for concurrent multiscale simulation : Aspectos da teoria peridinâmica discretizada e do método dos elementos finitos para simulação em múltiplas escalas concorrentes; Aspectos da teoria peridinâmica discretizada e do método dos elementos finitos para simulação em múltiplas escalas concorrentes

Fonte: Biblioteca Digital da Unicamp
Publicador: Biblioteca Digital da Unicamp

Tipo: Tese de Doutorado
Formato: application/pdf

Publicado em 28/02/2013
Português

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#Métodos de simulação#Multiescala#Método dos elementos finitos#Mecânica da fratura#Dinâmica molecular#Simulation methods#Multiescale#Finite element method#Fracture mechanics#Molecular dynamics

Nesse trabalho, considera-se a simulação em múltiplas escalas concorrentes, usando a teoria peridinâmica e a elasticidade clássica, para a simulação de problemas de engenharia. Primeiramente a teoria peridinâmica em uma dimensão é estudada em detalhes com o foco na aplicação de condições de contorno de Dirichlet. Problemas de estado plano de tensão em chapas com e sem furo são considerados. É proposto um método de pós-processamento dos resultados de peridinâmica para o cálculo das tensões no material. Em seguida, a peridinâmica discretizada é acoplada ao método dos elementos finitos por meio de dois diferentes programas de computador, um especializado em peridinâmica e o outro em elementos finitos. A modelagem acoplada é usada para prever a formação e a propagação de uma trinca em uma chapa com furo. O fenômeno macroscópico de formação e propagação de trincas é resultado de processos físicos com origem na escala atomística. No entanto, as simulações existentes deste tipo problema são normalmente feitas com abordagens baseadas na teoria do contínuo, como a mecânica da fratura e o dano contínuo, que não consideram aspectos atomísticos do problema. A teoria peridinâmica é uma formulação da mecânica do contínuo em termos de equações integrais...

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## ‣ Simulation results of a shunt active power filter with control based on p-q theory

Fonte: Universidade do Minho
Publicador: Universidade do Minho

Tipo: Conferência ou Objeto de Conferência

Publicado em /04/2003
Português

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#Power quality improvement#Harmonics compensation#Shunt active filter#p-q theory#Computer simulation

The present paper describes a shunt active power filter with a control system based on the p-q theory, and studies its performance through simulation results obtained with different types of loads.
It is explained, in a brief form, the p-q theory and its application in the control of a shunt active power filter. Matlab/Simulink was the simulation tool, used in the study, development, and performance evaluation of the shunt active power filter controller. The simulations were carried out for different loads, of linear and non-linear types.
The shunt active power filter allows compensating harmonic currents, reactive power, unbalanced loads, and zero-sequence currents, presenting a good dynamic and steady-state performance, as it can be observed in the simulation results.; Fundação para a Ciência e a Tecnologia (FCT) - POCTI/ESE/41170/2001.

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## ‣ Theory and Simulation of Water Permeation in Aquaporin-1

Fonte: Biophysical Society
Publicador: Biophysical Society

Tipo: Artigo de Revista Científica

Publicado em /01/2004
Português

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We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 × 10−14 cm3/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures ∼12. This number is explained in terms of channel architecture and conduction mechanism.

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## ‣ Enumeration of Oligomerization States of Membrane Proteins in Living Cells by Homo-FRET Spectroscopy and Microscopy: Theory and Application

Fonte: Biophysical Society
Publicador: Biophysical Society

Tipo: Artigo de Revista Científica

Publicado em 01/05/2007
Português

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Protein-protein interactions play a pivotal role in biological signaling networks. It is highly desirable to perform experiments that can directly assess the oligomerization state and degree of oligomerization of biological macromolecules in their native environment. Homo-FRET depends on the inverse sixth power of separation between interacting like fluorophores on the nanometer scale and is therefore sensitive to protein oligomerization. Homo-FRET is normally detected by steady-state or time-resolved fluorescence anisotropy measurements. Here we show by theory and simulation that an examination of the extent of homotransfer as measured by steady-state fluorescence anisotropy as a function of fluorophore labeling (or photodepletion) gives valuable information on the oligomerization state of self-associating proteins. We examine random distributions of monomers, dilute solutions of oligomers, and concentrated solutions of oligomers. The theory is applied to literature data on band 3 protein dimers in membranes, GPI-linked protein trimers in “rafts,” and clustered GFP-tagged epidermal growth factor receptors in cell membranes to illustrate the general utility and applicability of our analytical approach.

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## ‣ Step Length Measurement—Theory and Simulation for Tethered Bead Constant-Force Single Molecule Assay

Fonte: The Biophysical Society
Publicador: The Biophysical Society

Tipo: Artigo de Revista Científica

Português

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Linear molecular motors translocate along polymeric tracks using discrete steps. The step length is usually measured using constant-force single molecule experiments in which the polymer is tethered to a force-clamped microsphere. During the enzymatic cycle the motor shortens the tether contour length. Experimental conditions influence the achievable step length resolution, and ideally experiments should be conducted with high clamp-force using slow motors linked to small beads via stiff short tethers. We focus on the limitations that the polymer-track flexibility, the thermal motion of the microsphere, and the motor kinetics pose for step-length measurement in a typical optical tweezers experiment. An expression for the signal/noise ratio in a constant-force, worm-like chain tethered particle, single-molecule experiment is developed. The signal/noise ratio is related to the Fourier transform of the pairwise distance distribution, commonly used to determine step length from a time-series. Monte Carlo simulations verify the proposed theory for experimental parameter values typically encountered with molecular motors (polymerases and helicases) translocating along single- or double-stranded nucleic acids. The predictions are consistent with recent experimental results for double-stranded DNA tethers. Our results map favorable experimental conditions for observing single motor steps on various substrates but indicate that principal resolution limits are set by thermal fluctuations.

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## ‣ Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System

Fonte: The Biophysical Society
Publicador: The Biophysical Society

Tipo: Artigo de Revista Científica

Publicado em 08/04/2009
Português

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Ligand-induced receptor aggregation is a well-known mechanism for initiating intracellular signals but oligomerization of distal signaling molecules may also be required for signal propagation. Formation of complexes containing oligomers of the transmembrane adaptor protein, linker for the activation of T cells (LAT), has been identified as critical in mast cell and T cell activation mediated by immune response receptors. Cross-linking of LAT arises from the formation of a 2:1 complex between the adaptor Grb2 and the nucleotide exchange factor SOS1, which bridges two LAT molecules through the interaction of the Grb2 SH2 domain with a phosphotyrosine on LAT. We model this oligomerization and find that the valence of LAT for Grb2, which ranges from zero to three, is critical in determining the nature and extent of aggregation. A dramatic rise in oligomerization can occur when the valence switches from two to three. For valence three, an equilibrium theory predicts the possibility of forming a gel-like phase. This prediction is confirmed by stochastic simulations, which make additional predictions about the size of the gel and the kinetics of LAT oligomerization. We discuss the model predictions in light of recent experiments on RBL-2H3 and Jurkat E6.1 cells and suggest that the gel phase has been observed in activated mast cells.

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## ‣ Theory and simulation on the kinetics of protein–ligand binding coupled to conformational change

Fonte: American Institute of Physics
Publicador: American Institute of Physics

Tipo: Artigo de Revista Científica

Português

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Conformational change during protein–ligand binding may significantly affect both the binding mechanism and the rate constant. Most earlier theories and simulations treated conformational change as stochastic gating with transition rates between reactive and nonreactive conformations uncoupled to ligand binding. Recently, we introduced a dual-transition-rates model in which the transition rates between reactive and nonreactive conformations depend on the protein–ligand distance [H.-X. Zhou, Biophys. J. 98, L15 (2010)]. Analytical results of that model showed that the apparent binding mechanism switches from conformational selection to induced fit, when the rates of conformational transitions increase from being much slower than the diffusional approach of the protein–ligand pair to being much faster. The conformational-selection limit (kCS) and the induced-fit limit (kIF) provide lower and upper bounds, respectively, for the binding rate constant. Here we introduce a general model in which the energy surface of the protein in conformational space is coupled to ligand binding, and present a method for calculating the binding rate constant from Brownian dynamics simulations. Analytical and simulation results show that, for an energy surface that switches from favoring the nonreactive conformation while the ligand is away to favoring the reactive conformation while the ligand is near...

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## ‣ Theory and Simulation of Multicomponent Osmotic Systems

Fonte: PubMed
Publicador: PubMed

Tipo: Artigo de Revista Científica

Português

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Most cellular processes occur in systems containing a variety of components many of which are open to material exchange. However, computer simulations of biological systems are almost exclusively performed in systems closed to material exchange. In principle, the behavior of biomolecules in open and closed systems will be different. Here, we provide a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the Kirkwood-Buff (KB) theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly2 and Gly3 in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. In addition, KB theory is used to help rationalize the aggregation properties of the solutes. Here one observes that the picture of solute association described by the KB integrals, which are directly related to the solution thermodynamics, and that provided by more physical clustering approaches are different. It is argued that the combination of KB theory and simulation data provides a simple and powerful tool for the analysis of complex multicomponent open and closed systems.

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## ‣ Theory and simulation of amorphous organic electronic devices

Fonte: Massachusetts Institute of Technology
Publicador: Massachusetts Institute of Technology

Tipo: Tese de Doutorado
Formato: 478 p.

Português

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The electronic properties of amorphous organic thin films are of great interest due to their application in devices such as light emitting devices, solar cells, photodetectors, and lasers. Compared to conventional inorganic semiconductors, amorphous organic thin films have the potential to enable entirely new functionality, larger areas, higher efficiencies, flexible substrates, and inexpensive fabrication. The development of amorphous organic electronic devices requires a deep understanding of the physics of the underlying electronic processes, which are controlled by the behavior of polarons (charged molecular states), and excitons (neutral molecular excited states). In this thesis we employ microscopic models of polaron and exciton processes to calculate macroscale phenomena in amorphous small molecular weight organic thin films using Monte Carlo (MC) simulations. The principle results that we report are: (1) the experimental demonstration and theoretical analysis of the previously neglected phenomenon of solid state solvation; (2) the identification of significant errors in existing models of molecular energy level disorder in polarizible media;; (cont.) (3) the most rigorously self-consistent quantitative fit of a dispersive exciton diffusion model to experimental data from a small molecular weight amorphous organic solid; (4) MC simulations of equilibrium polaron mobilities in amorophous organic solids as a function of both field and carrier concentration; and (5) MC simulations of space charge limited (SCL) currents through thin films as a function of voltage under typical operating device conditions. To our knowledge...

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## ‣ Stochastic Modeling and Simulation of Biological Phenomena with Applications in Population Genetics and in Cell Populations

Fonte: Universidade Rice
Publicador: Universidade Rice

Português

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#Stochastic process#Simulation#Statistical genomics#Population genetics#Cell population#Mathematical modeling

Stochastic modeling and simulation play important roles in population genetics, statistical genetics, cell biology, molecular biology and evolutionary theory. This thesis explores four aspects of stochastic modeling and simulation of biological phenomena with applications.
Research carried out is focused on two major themes. The first one (Chapters 2 and 3) concerns application of stochastic modeling in genetics, specifically to identify biases in analysis of genetics data. Two problems that are considered are ascertainment bias in estimation of microsatellite diversity in interspecies comparisons, and sample-selection bias in comparing different methods of rare variant analysis. The second theme (Chapters 4 and 5) concerns application of Poisson and branching process models to understand various aspects of cell proliferation, using S-phase labeling. Two model systems are: transient dynamics of proliferation of neurogenic progenitors in mouse brain with emphasis on differentiation and apoptosis, and balanced growth under different assumptions concerning DNA-replication pattern.
In the first part, we investigate factors that are influencing the ascertainment bias of microsatellite allele sizes and explore the impact on estimates of mutation rates. Microsatellite loci play an important role as markers for identification...

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## ‣ Model-based Adaptive Algorithms for Time-Varying Communication Channels with Application to Adaptive Multiuser Detection

Fonte: Institute of Electrical and Electronics Engineers (IEEE Inc)
Publicador: Institute of Electrical and Electronics Engineers (IEEE Inc)

Tipo: Conference paper

Português

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#Keywords: Algorithms#Channel capacity#Communication channels (information theory)#Computer simulation#Mathematical models#Time varying systems#Adaptive multiuser detection#Degenerate algorithms#Multiuser receivers#Adaptive algorithms

This paper shows through theory and simulation the superiority of model-based adaptive algorithms relative to observation-only-based adaptive algorithms, such as LMS and RLS, when applied to tracking time-varying channels. The model-based formulation reve

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## ‣ Theory and Simulation of Magnetic Materials: Physics at Phase Frontiers

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 18/09/2013
Português

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The combination of theory and simulation is necessary in the investigation of
properties of complex systems where each method alone cannot do the task
properly. Theory needs simulation to test ideas and to check approximations.
Simulation needs theory for modeling and for understanding results coming out
from computers. In this review, we give recent examples to illustrate this
necessary combination in a few domains of interest such as frustrated spin
systems, surface magnetism, spin transport and melting. Frustrated spin systems
have been intensively studied for more than 30 years. Surface effects in
magnetic materials have been widely investigated also in the last three
decades. These fields are closely related to each other and their spectacular
development is due to numerous applications. We confine ourselves to
theoretical developments and numerical simulations on these subjects with
emphasis on spectacular effects occurring at frontiers of different phases.

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## ‣ Diffusive epidemic process: theory and simulation

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 07/08/2006
Português

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We study the continuous absorbing-state phase transition in the
one-dimensional diffusive epidemic process via mean-field theory and Monte
Carlo simulation. In this model, particles of two species (A and B) hop on a
lattice and undergo reactions B -> A and A + B -> 2B; the total particle number
is conserved. We formulate the model as a continuous-time Markov process
described by a master equation. A phase transition between the (absorbing)
B-free state and an active state is observed as the parameters (reaction and
diffusion rates, and total particle density) are varied. Mean-field theory
reveals a surprising, nonmonotonic dependence of the critical recovery rate on
the diffusion rate of B particles. A computational realization of the process
that is faithful to the transition rates defining the model is devised,
allowing for direct comparison with theory. Using the quasi-stationary
simulation method we determine the order parameter and the survival time in
systems of up to 4000 sites. Due to strong finite-size effects, the results
converge only for large system sizes. We find no evidence for a discontinuous
transition. Our results are consistent with the existence of three distinct
universality classes, depending on whether A particles diffusive more rapidly...

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## ‣ Theory and simulation of gelation, arrest and yielding in attracting colloids

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 29/03/2004
Português

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We present some recent theory and simulation results addressing the phenomena
of colloidal gelation at both high and low volume fractions, in the presence of
short-range attractive interactions. We discuss the ability of mode-coupling
theory and its adaptations to address situations with strong heterogeneity in
density and/or dynamics. We include a discussion of the effect of attractions
on the shear-thinning and yield behaviour under flow.; Comment: 17 pages, 6 figures

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## ‣ Theory and Simulation of Multiphase Polymer Systems

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 08/01/2010
Português

Relevância na Pesquisa
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The theory of multiphase polymer systems has a venerable tradition. The
'classical' theory of polymer demixing, the Flory-Huggins theory, was developed
already in the forties of the last century. It is still the starting point for
most current approaches -- be they improved theories for polymer
(im)miscibility that take into account the microscopic structure of blends more
accurately, or sophisticated field theories that allow to study inhomogeneous
multicomponent systems of polymers with arbitrary architectures in arbitrary
geometries. In contrast, simulations of multiphase polymer systems are
relatively young. They are still limited by the fact that one must simulate a
large number of large molecules in order to obtain meaningful results. Both
powerful computers and smart modeling and simulation approaches are necessary
to overcome this problem.
This article gives an overview over the state-of-the art in both areas,
theory and simulation. While the theory has reached a fairly mature stage by
now, and many aspects of it are covered in textbooks on polymer physics, the
information on simulations is much more scattered. This is why some effort has
been invested into putting together a representative list of references in this
area (up to the year of 2008) -- which is of course still far from complete.; Comment: 63 pages...

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## ‣ Theory and simulation of quantum photovoltaic devices based on the non-equilibrium Green's function formalism

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 12/06/2012
Português

Relevância na Pesquisa
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This article reviews the application of the non-equilibrium Green's function
formalism to the simulation of novel photovoltaic devices utilizing quantum
confinement effects in low dimensional absorber structures. It covers
well-known aspects of the fundamental NEGF theory for a system of interacting
electrons, photons and phonons with relevance for the simulation of
optoelectronic devices and introduces at the same time new approaches to the
theoretical description of the elementary processes of photovoltaic device
operation, such as photogeneration via coherent excitonic absorption,
phonon-mediated indirect optical transitions or non-radiative recombination via
defect states. While the description of the theoretical framework is kept as
general as possible, two specific prototypical quantum photovoltaic devices, a
single quantum well photodiode and a silicon-oxide based superlattice absorber,
are used to illustrated the kind of unique insight that numerical simulations
based on the theory are able to provide.; Comment: 20 pages, 10 figures; invited review paper

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## ‣ Static and Dynamic Anomalies in a Repulsive Spherical Ramp Liquid: Theory and Simulation

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 10/11/2004
Português

Relevância na Pesquisa
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We compare theoretical and simulation results for static and dynamic
properties for a model of particles interacting via a spherically symmetric
repulsive ramp potential. The model displays anomalies similar to those found
in liquid water, namely, expansion upon cooling and an increase of diffusivity
upon compression. In particular, we calculate the phase diagram from the
simulation and successfully compare it with the phase diagram obtained using
the Rogers-Young (RY) closure for the Ornstein-Zernike equation. Both the
theoretical and the numerical calculations confirm the presence of a line of
isobaric density maxima, and lines of compressibility minima and maxima.
Indirect evidence of a liquid-liquid critical point is found. Dynamic
properties also show anomalies. Along constant temperature paths, as the
density increases, the dynamics alternates several times between slowing down
and speeding up, and we associate this behavior with the progressive
structuring and de-structuring of the liquid. Finally we confirm that mode
coupling theory successfully predicts the non-monotonic behavior of dynamics
and the presence of multiple glass phases, providing strong evidence that
structure (the only input of mode coupling theory) controls dynamics.; Comment: Static and Dynamic Anomalies in a Repulsive Spherical Ramp Liquid:
Theory and Simulation

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## ‣ Distribution and diffusivity of a hydrophobic probe molecule in the interior of a membrane: theory and simulation

Fonte: Rockefeller University Press
Publicador: Rockefeller University Press

Tipo: Artículo
Formato: 1231671 bytes; application/pdf

Português

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We propose a simple model for the distribution of position and orientation and the diffusion of a hydrophobic probe molecule embedded in a membrane. The molecule experiences both a Maier-Saupe orienting potential as well as an enclosing potential of repulsion from the membrane walls. A statistical thermodynamics treatment of the model provides predictions of the location and orientation of the molecule within the membrane. In particular, we evaluate the order parameter of the molecule in terms of the model constants. The diffusivity of the probe is studied by Brownian dynamics simulation. For rotational diffusion, we check an available analytical approximate treatment that allows for the prediction of the dynamics in terms of equilibrium quantities. We also pay attention to quantities related to the initial and mean reorientational rate of the probe. For translational diffusion, we use the simulation results to analyze some general aspects of lateral and transversal diffusion.; Support was provided by grants ERBCII*CT940124 (European Commission),
and PB93-1132 (DGICYT-MEC) to JGT, and PB93-0126 (DGICYT-
MEC) to AUA. A predoctoral grant from DGICYT-MEC awarded to
MLH is also acknowledged.; Peer reviewed

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## ‣ Estimates for the pressure and thermal distortions of coating dies for use in design and simulation

Fonte: Rochester Instituto de Tecnologia
Publicador: Rochester Instituto de Tecnologia

Tipo: Tese de Doutorado

Português

Relevância na Pesquisa
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#Beam theory#Coating die#Deflection and flow coupled#Finite element analysis#TA455.P58 S44 2010#Polymer engineering#Plastic coating#Dies (Metal-working)--Design and construction#Dies (Metal-working)--Thermal properties#Fluid dynamics

A coating die is used for distributing liquid in order to apply a uniform film on a solid surface. The fluid flowing through the die cavity can exert a pressure of up to 500,000 Pascal on the die body. This liquid pressure can distort the die and lead to a non-uniform slot opening, which in turn causes non-uniformity in the coating thickness. Distortion of the die can also occur during non-isothermal operation of the die; this is an undesired consequence of delivering liquids at a different temperature than the die itself. The distortions undergone by the die both due to liquid pressure and non-isothermal conditions should be within the manufacturing tolerances for the slot heights in order to maintain uniformity in the coating.
The deformation exhibited by a coating die due to pressure loadings is modeled both two-dimensionally and three-dimensionally. A two-dimensional model has lower computational load and is preferred for die design. For the two-dimensional analysis of a coating die, the finite element method is used to determine the deflections due to pressure loadings with a focus on slot heights. A model of low computational load is also developed based on beam theory, and its results are compared with those of the two-dimensional finite element analyses predictions. The beam model is incorporated in a die design and simulation program in which flow and slot deformations are coupled. Two-dimensional finite element analyses due to non-isothermal conditions are also performed on the coating die to give an estimate of the die deflection due to temperature variations within the die. A three-dimensional coating die with varying inner cavity area is modeled and analyzed to check its predictions with those of the two-dimensional finite element analyses and beam theory results.
In the literature reviewed...

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