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- Sociedade Brasileira de Física
- Brazilian Society of Chemical Engineering
- Universidade Rice
- Tech Science Press
- Águas de Lindóia
- Royal Society of London
- American Chemical Society
- Taylor & Francis Group
- American Physical Society
- Mineralogical Society of America
- Rochester Instituto de Tecnologia
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## O modelo de Uhlenbeck-Ford e cálculos de energia livre de sistemas na fase fluida; The Uhlenbeck-Ford model and free-energy calculations for fluid phase systems

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

Tipo: Dissertação de Mestrado
Formato: application/pdf

Publicado em 26/06/2015
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#Cálculo de energia livre#Líquidos#Simulação molecular#Free energy calculations#Liquids#Molecular simulations

Neste trabalho, apresentamos um estudo a respeito do modelo de Uhlenbeck-Ford como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, utilizando metodos de simulacao molecular. Este sistema artificial, que e caracterizado por um potencial puramente repulsivo e que diverge rapidamente, foi originalmente proposto como um modelo para o estudo teorico de gases imperfeitos. Este modelo foi motivado pelo fato de que todas as integrais de muitos corpos, envolvidas no calculo dos coeficientes viriais, podem ser facilmente calculadas analiticamente. Entretanto apenas oito coeficientes eram conhecidos. Dois novos coeficientes (..10 e ..11) foram determinados para o modelo neste trabalho, alem de uma expressao essencialmente exata para a equacao de estado e energia livre de Helmholtz em funcao de um parametro adimensional. Este nos permitira reunir todas as informacoes a respeito da energia livre do sistema em uma unica expressao, independentemente da escolha de parametros do potencial. Por fim, exploraremos a aplicabilidade deste modelo como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, usando tecnicas de simulacao molecular a partir de processos fora de equilibrio. Nossos resultados para o fluido de Lennard-Jones e para o silicio liquido...

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## Gibbs free energy of transfer of a methylene group on {UCON + (sodium or potassium) phosphate salts} aqueous two-phase systems: Hydrophobicity effects

Fonte: Elsevier Ltd.
Publicador: Elsevier Ltd.

Tipo: Artigo de Revista Científica

Publicado em /08/2010
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The Gibbs free energy of transfer of a suitable hydrophobic probe can be regarded as a measure of the
relative hydrophobicity of the different phases. The methylene group (CH2) can be considered hydrophobic,
and thus be a suitable probe for hydrophobicity. In this work, the partition coefficients of a series of
five dinitrophenylated-amino acids were experimentally determined, at 23 °C, in three different tie-lines
of the biphasic systems: (UCON + K2HPO4), (UCON + potassium phosphate buffer, pH 7), (UCON +
KH2PO4), (UCON + Na2HPO4), (UCON + sodium phosphate buffer, pH 7), and (UCON + NaH2PO4). The
Gibbs free energy of transfer of CH2 units were calculated from the partition coefficients and used to compare
the relative hydrophobicity of the equilibrium phases. The largest relative hydrophobicity was found
for the ATPS formed by dihydrogen phosphate salts.; Fundação para a Ciência e a Tecnologia (FCT) - Programa "Ciência 2007", SFRH/BD/43439/2008; LSRE; FEDER/POCI/2010

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## Simple measurement of surface free energy using a web cam

Fonte: Sociedade Brasileira de Física
Publicador: Sociedade Brasileira de Física

Tipo: Artigo de Revista Científica
Formato: text/html

Publicado em 01/09/2012
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In this paper we describe a simple and pedagogical experiment to measure surface free energy (SFE), which is a mainstream subject to teach undergraduate and graduate level Physics science. Beyond this, the advantage of this work relies on the simplicity of the materials used, namely non-harmful and low cost products such as water, glycerol, ethylene glycol and propanol, offering a useful pedagogical opportunity to discuss basic but relevant concepts regarding surface science phenomena. As example, contact angle measurements were used to estimate SFE and the wetting behavior of distinct solid surfaces such as glass and polytetrafluoroethylene (PTFE, Teflon®).

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## Application of interval analysis for gibbs and helmholtz free energy global minimization in phase stability analysis

Fonte: Brazilian Society of Chemical Engineering
Publicador: Brazilian Society of Chemical Engineering

Tipo: Artigo de Revista Científica
Formato: text/html

Publicado em 01/03/2006
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The tangent plane criterion has become important for a correct solution evaluation phase and chemical of equilibrium problem. This method, applicable to single and multiphase systems, is mainly used for a single equation of state modeling all phases involved. The present work is mainly concerned with the application of interval analysis methods for global energy minimization in high-pressure phase stability problems. Two approaches are applied: (i) the Gibbs free energy global minimization under conditions of constant temperature and pressure and (ii) the Helmholtz free energy density global minimization under conditions of constant temperature and volume. Five case studies, one ternary and four binary systems, are analyzed in connection with the Peng-Robinson equation of state (PREOS) model. Five more case studies, for the CO2 + trans-2-hexen-1-ol system at high pressures, are used to compare different methods of phase equilibrium calculation with the approach using interval analysis. Finally, a complex system, clove oil + CO2, is analyzed. The results indicate that the interval analysis method is robust and reliable for all the problems studied.

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## Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem

Fonte: Universidade Rice
Publicador: Universidade Rice

Português

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Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine
equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits
unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

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## DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy

Fonte: Universidade Rice
Publicador: Universidade Rice

Português

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#Free energy landscape#Crooks fluctuation theorem#Single molecule manipulation#Jarzynski equality#Equilibrium#Nonequilibrium#Poly(da)#Atomic force microscopy#Self-assembly#RNA#Nanostructure

There is an important conceptual lesson which has long been appreciated by those
who work in biophysics and related interdisciplinary fields. While the extraordinary
behavior of biological matter is governed by its detailed atomic structure and random
fluctuations, and is therefore difficult to predict, it can nevertheless be understood
within simplified frameworks. Such frameworks model the system as consisting of only
one or a few components, and model the behavior of the system as the occupation
of a single state out of a small number of states available. The emerging widespread
application of nanotechnology, such as atomic force microscopy (AFM), has expanded
this understanding in eye-opening new levels of detail by enabling nano-scale control,
measurement, and visualization of biological molecules. This thesis describes two
independent projects, both of which illuminate this understanding using AFM, but
which do so from very different perspectives.
The organization of this thesis is as follows. Chapter 1 begins with an experimental
background and introduction to AFM, and then describes our setup in both
single-molecule manipulation and imaging modes. In Chapter 2, we describe the
first project, the motivation for which is to extend methods for the experimental
determination of the free energy landscape of a molecule. This chapter relies on
the analysis of single-molecule manipulation data. Chapter 3 describes the second
project...

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## Experimental Free Energy Landscape Reconstruction of DNA Unstacking Using Crooks Fluctuation Theorem

Fonte: Universidade Rice
Publicador: Universidade Rice

Português

Relevância na Pesquisa

65.81%

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine
equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits
unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

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## A new free energy-based model of the kinematic hardening in large strain elastoplasticity

Fonte: Tech Science Press
Publicador: Tech Science Press

Tipo: Artigo de Revista Científica

Publicado em //2005
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In this paper, a free energy-based formulation incorporating the effect of kinematic hardening is proposed. The formulation is able to reproduce symmetric expressions for the back stress while incorporating the multiplicative decomposition of the deformation gradient. Kinematic hardening is combined with isotropic hardening where an associative flow rule and von Mises yield criterion are applied. An accurate and trivial wise objective integration algorithm employing the exponential map is developed. In order to ensure a high convergence rate in the global iteration approach, an algorithmic tangent operator is derived. The computational algorithm is implemented and applied to a shell finite element which allows the use of complete three-dimensional constitutive laws. Robustness and efficiency of the proposed algorithm are demonstrated by numerical examples.; http://www.techscience.com/cmes/2005/v8n1_index.html; Igor Kar saj, Carlo Sansour and Jurica Sori 'c

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## Study of surface free energy on a lattice-gas model applied to Liquid bridge

Fonte: Águas de Lindóia
Publicador: Águas de Lindóia

Tipo: Poster ou Painel

Português

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The pulmonary crackling and the formation of liquid bridges are problems that for centuries have been attracting the attention of scientists. In order to study these phenomena, it was developed a canonical cubic lattice-gas like model to explain the rupture of liquid bridges in lung airways [A. Alencar et al., 2006, PRE]. Here, we further develop this model and add entropy analysis to study thermodynamic properties, such as free energy and force. The simulations were performed using the Monte Carlo method with Metropolis algorithm. The exchange between gas and liquid particles were performed randomly according to the Kawasaki dynamics and weighted by the Boltzmann factor. Each particle, which can be solid (s), liquid (l) or gas (g), has 26 neighbors: 6 + 12 + 8, with distances 1, √2 and √3, respectively. The energy of a lattice's site m is calculated by the following expression:
Em = ∑k=126 Ji(m)j(k) in witch (i, j) = g, l or s. Specifically, it was studied the surface free
energy of the liquid bridge, trapped between two planes, when its height is changed. For that, was considered two methods. First, just the internal energy was calculated. Then was considered the entropy. It was fond no difference in the surface free energy between this two methods. We calculate the liquid bridge force between the two planes using the numerical surface free energy. This force is strong for small height...

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## Characterisation of cellulose surface free energy

Fonte: VSP
Publicador: VSP

Tipo: Artigo de Revista Científica

Publicado em //1998
Português

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The thin-layer wicking technique was used to determine the surface free energy components and the surface character of three celluloses (Sigmacell 101, Sigmacell 20, and Avicel 101), using an appropriate form of the Washburn equation. For this purpose, the penetration rates of probe liquids into thin porous layers of the celluloses deposited onto horizontal glass plates were measured. It was found that the wicking was a reproducible process and that the thin-layer wicking technique could be used for the determination of the celluloses' surface free energy components. The size of the cellulose particles was characterized with the Galai CIS-100 system and their crystallinity was measured by X-ray diffraction. The three celluloses have high apolar (ys LW = 50-56 mJ/m²) and electron donor ys- = 42-45 mJ/m²) components, while the electron acceptor component (ys+) is pratically zero. The free energy interactions of cellulose/water/cellulose calculated from the components are positive, regardless of the cellulose crystallinity. This would mean that the cellulose surfaces have a hydrophilic character. However, the work of spreading of water has a small negative value (3-9 mJ/m²), indicating that the surfaces are slightly hydrophobic. It is believed that the work of spreading characterizes better the hydrophobicity of the surface than the free energy of particle/water/particle interaction...

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## Reduction efficiency prediction of CENIBRA's recovery boiler by direct minimization of gibbs free energy

Fonte: Brazilian Society of Chemical Engineering
Publicador: Brazilian Society of Chemical Engineering

Tipo: Artigo de Revista Científica
Formato: text/html

Publicado em 01/09/2008
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The reduction efficiency is an important variable during the black liquor burning process in the Kraft recovery boiler. This variable value is obtained by slow experimental routines and the delay of this measure disturbs the pulp and paper industry customary control. This paper describes an optimization approach for the reduction efficiency determination in the furnace bottom of the recovery boiler based on the minimization of the Gibbs free energy. The industrial data used in this study were directly obtained from CENIBRA's data acquisition system. The resulting approach is able to predict the steady state behavior of the chemical composition of the furnace recovery boiler, - especially the reduction efficiency when different operational conditions are used. This result confirms the potential of this approach in the analysis of the daily operation of the recovery boiler.

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## Free energy of the three-state τ2(tq) model as a product of elliptic functions

Fonte: Royal Society of London
Publicador: Royal Society of London

Tipo: Artigo de Revista Científica

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We show that the free energy of the three-state τ2(t q) model can be expressed as products of Jacobi elliptic functions, the arguments being those of an hyperelliptic parametrization of the associated chiral Potts model. This is the first application of

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## Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method

Fonte: American Chemical Society
Publicador: American Chemical Society

Tipo: Artigo de Revista Científica

Português

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#Keywords: fructose 1,6 bisphosphatase inhbitor#fructose bisphosphatase#unclassified drug#article#binding affinity#binding site#calculation#drug structure#energy#enzyme activity#enzyme binding

Relative solvation and binding free energies were calculated for a series of fructose-1,6-bisphosphatase inhibitors using a free energy perturbation (FEP) method that uses quantum mechanics (QM) for treating the inhibitors and molecular mechanics (MM) for

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## Deterministic derivation of non-equilibrium free energy theorems for natural isothermal isobaric systems

Fonte: Taylor & Francis Group
Publicador: Taylor & Francis Group

Tipo: Artigo de Revista Científica

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#Keywords: Computer simulation#Isotherms#Molecular dynamics#Phase equilibria#Statistical mechanics#Theorem proving#Barostatting#Free energy theorems#Isobaric systems#Free energy Fluctuation theorem#Jarzynski equality

The non-equilibrium free energy theorems show how distributions of work along non-equilibrium paths are related to free energy differences between the equilibrium states at the end points of these paths. In this paper we develop a natural way of barostatt

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## Nonequilibrium Free-Energy Relations for Thermal Changes

Fonte: American Physical Society
Publicador: American Physical Society

Tipo: Artigo de Revista Científica

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#Keywords: Reservoirs (water)#(Liquid + liquid) equilibrium#(Skew) free energy#American Physical Society (APS)#Crooks fluctuation theorem#Fixed temperature#Jarzynski equality#Non equilibrium#nonequilibrium free-energy#Out of equilibrium#Path integrals

The Jarzynski equality and the Crooks fluctuation theorem enable the calculation of the change in a system's free energy from nonequilibrium path integrals. These relations consider processes where the system is driven out of equilibrium by a mechanical e

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## Free energy of formation of zircon and hafnon

Fonte: Mineralogical Society of America
Publicador: Mineralogical Society of America

Tipo: Artigo de Revista Científica

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#Keywords: baddeleyite#cristobalite#electrochemical method#enthalpy#entropy#fayalite#phase transition#zircon Fayalite#Free energy of formation#Hafnon#Thermodynamic data

The free energy of formation of zircon (ZrSiO4) from its oxides was determined between 1100 and 1300 K by an electrochemical method, in which values of μ02 defined by the two assemblages Fe2SiO4-Fe-SiO2 (fayalite-iron-quartz) and Fe2SiO4- Fe-ZrO2-ZrSiO4

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## Theoretical prediction of free-energy landscapes for complex self-assembly

Fonte: AIP
Publicador: AIP

Tipo: Article; accepted version

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This is the accepted manuscript. Copyright (2015) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in The Journal of Chemical Physics 142, 021101 (2015) and may be found at http://doi.org/10.1063/1.4905670; We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.; W.M.J. acknowledges support from the Gates Cambridge Trust and the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1143678. D.F. acknowledges European Research Council Advanced Grant No. 227758 and Engineering and Physical Sciences Research Council Programme Grant No. EP/I001352/1. Research carried out in part at the Center for Functional Nanomaterials...

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## Variable temperature NMR studies on 3-imino-2,2,4,4-tetramethylcyclobutanones: Gibbs free energy for inversion of groups on nitrogen

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

Tipo: Tese de Doutorado

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#Chemistry#Free energy#Gibbs free energy#Molecular structure#Orbital location#QD181.N1 C56 2003#Organonitrogen compounds--Research#Imines--Research#Imino compounds--Research#Gibbs' free energy#Nuclear magnetic resonance spectroscopy

A value for the free energy of activation, or G for the inversion of groups on
the imino nitrogen of the title compounds was calculated from data obtained from
variable temperature NMR. The coalescence temperature, Tc, is obtained as the
temperature at which the non-equivalent methyl resonances of the title compounds
collapse to a singlet. G is calculated from
G =2.3RTc(10.32 + logTc/k) Eq.3
derived from the Eyring Equation.
p-Methoxyphenylimino-2,2,4,4-tetramethyl 3-cyclobutanone (4) is found to
possess an energy of activation equal to that of 18.55 kcal/mole with its temperature of
coalescence at 118C.
p-Nitrophenylimino-2,2,4,4-tetramethyl 3-cyclobutanone (5) is found to have an
energy of activation for inversion to be 14.25 kcal/mole. The coalescence temperature
found for the nitro derivative was found to be subsequently lower than that of the
methoxy, 35C.
The G
value of N-(2,2,4,4-tetramethyl-3 -cyclobutanone)-p-toluenesulfonamide
(16) was found to have a value no greater than 16.42 kcal/mole with a corresponding Tc
value of 76C.
Whereas, the N-(3,3-Dichloro-2,2,4,4-tetramethyl-3-cyclobutanone)-
toluenesulfonamide (17) yielded a value of 15.32 kcal/mole for the inversion energy.
The Tc was found to be 56C.
The data support the hypothesis that lone pair orbital interaction in the transition state
affect the free energy of inversion of groups attached to the imino nitrogen.

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## The inverse relation method for obtaining the free energy of the chiral Potts model

Fonte: Elsevier
Publicador: Elsevier

Tipo: Artigo de Revista Científica

Português

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#Keywords: Algebra#Mathematical models#Statistical mechanics#Inversion relation method#Free energy Chiral Potts model#Free energy#Lattice models#Statistical mechanics

We derive the free energy of the chiral Potts model by the infinite lattice "inversion relation" method. This method is non-rigorous in that it always needs appropriate analyticity assumptions. Guided by previous calculations based on exact finite-lattice functional relations, we find that in addition to the usual assumption that the free energy be analytic and bounded in some principal domain of the rapidity parameter space that includes the physical regime, we also need a much less obvious symmetry. We can then obtain the free energy by Wiener-Hopf factorization in the complex planes of appropriate variables. Together with the inversion relation, this symmetry relates the values of the free energy in all neighbouring domains to those in the principal domain.

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## A non-equilibrium free energy theorem for deterministic systems

Fonte: Taylor & Francis Group
Publicador: Taylor & Francis Group

Tipo: Artigo de Revista Científica

Português

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#Keywords: Free energy#Hamiltonians#Mathematical transformations#Phase equilibria#Probability#Thermodynamic properties#Deterministic systems#Fluctuation theorem#Logarithms#Molecular physics

Jarzynski and Crooks have recently shown that equilibrium free energy differences can be computed from non-equilibrium thermodynamic path integrals. In the present paper we give a new derivation of this extraordinary relation. Our derivation which is valid for time reversible deterministic systems highlights the close relationship between the non-equilibrium free energy theorems and the fluctuation theorem.

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