Molecular simulation

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Excess Thermodynamic Properties of Chainlike Mixtures. 1. Predictions from the Soft−SAFT Equation of State and Molecular Simulation

Excess Thermodynamic Properties of Chainlike Mixtures. 1. Predictions from the Soft−SAFT Equation of State and Molecular Simulation

The aim of the present work is to calculate excess thermo- dynamic properties of binary mixtures of Lennard-Jones chains using Monte Carlo simulation and the Soft - SAFT molecular- based equation of state. The theortical results obtained from the theory are compared to exact molecular simulation data. This allows us to check the accuracy of the equation of state for predicting excess functions. In particular, we have investi- gated the influence of segment size, dispersive energy, and chain length on excess properties, such as the excess volume, configurational internal energy, and heat.
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10 Lee mas

A combined experimental and molecular simulation study of factors influencing interaction of quinoa proteins–carrageenan

A combined experimental and molecular simulation study of factors influencing interaction of quinoa proteins–carrageenan

Foods are complex systems composed among other components of proteins and polysaccharides. These two biopolymers play an impor- tant role on the food structure, characteristics and stability due to their functional and textural properties [1]. In particular, protein in food is gaining more value due to its capacity to act on several different hi- erarchical structural scales from the molecular (where the functional properties depend directly on the protein structure) to a mesoscale (where the function depends on the ability of proteins to interact, form and stabilize mesostructures) and macroscale (where the function is an interplay of mesostructures). This new hierarchical model to de- fine the functional properties of food proteins is based on the structural length scale required for them to achieve a particular function [2].
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9 Lee mas

Organoleptical properties of natural, non caloric sweeteners : molecular simulation, mixture optimization and experimental validation in carbonated soft drinks

Organoleptical properties of natural, non caloric sweeteners : molecular simulation, mixture optimization and experimental validation in carbonated soft drinks

Transduction of bitter taste in humans is mediated by ∼25 receptors of the hTAS2R gene family, also known as hT2R (Figure 1-3)(M. Behrens & Meyerhof, 2006). The hT2Rs are members of the large family of GPCRs. Due to low sequence similarity of T2Rs with class A GPCR, classification is somewhat ambiguous, but most analysis support the classification of T2Rs as class A GPCRs (Nordström, Sällman Almén, Edstam, Fredriksson, & Schiöth, 2011; DiPizio & Niv, 2014). The activation mechanism in this subfamily are poorly understood (Upadhyaya et al., 2010). In structural terms, hT2Rs contain between 290 and 333 amino acids, which are composed by a short extracellular domain at the amino end and a seven-transmembrane helical domain on the carboxyl end. GLY28 and SER285 residues are highly conserved in transmembrane domains 1 and 7 of hT2Rs, according to amino acid sequence analysis and molecular modeling studies. These residues could play an important role in receptor activation mediated by the formation of hydrogen bonding between the residues. However, only GLY28 is conserved at the level of GPCR class A (Smith, 2010). Although the structure of hT2Rs receptors has not been solved, most of their 3D structures were predicted by comparative modeling, using as template the crystal structure of rhodopsin (member of class A GPCR) of different species. Despite limited sequence similarity, conserved residues in the transmembranal domain belong to binding sites for various compounds (Singh et al., 2011).
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140 Lee mas

A detailed study of cholinium chloride and levulinic acid deep eutectic solvent system for CO2 capture via experimental and molecular simulation approaches

A detailed study of cholinium chloride and levulinic acid deep eutectic solvent system for CO2 capture via experimental and molecular simulation approaches

H-bonding. Residence time was calculated from the exponential decay of the conditional probability for a site to stay within a sphere of defined radius around another molecular site, as explained in previous work. 103 Sun et al. 102 reported lifetimes of hydrogen bonds in reline DES, showing lifetimes lower than 13 ps for all the reported H-bonds in the eutectic composition, with values of 12.574 ps for the [CH] + –Cl H-bond, 2.397 ps for the urea (HBD)–[Cl] H-bond, and 2.952 ps for the urea–urea interaction. These values are lower than those reported for CHCL_LEV_1_2 in Fig. 14a, but it may be argued that the distance criteria used to define residence times in Fig. 14a (6.0 Å) is roughly double that used by Sun et al. 102 to define their H-bond lifetimes (roughly 3 Å). The criteria used in Fig. 14 consider the existence of a second solvation shell around each hydrogen bond donor site, and thus, although H-bonds are destroyed for distances larger than 3.0 Å, those atoms reamining in the 3–6 Å range arise from the reorgani- zation of the local H-bonding structure and they may develop a new H-bond in a fast way, and thus using 6.0 Å may give a realistic picture of the H-bonding around a certain site. The residence times reported in Fig. 14a are very similar for all the considered interactions being in the 35 to 55 ps range. Moreover, the analysis of the temperature evolution of residence times follows a similar non-Arrhenius pattern for all the studied interactions, thus confirming a strong correlation between the dynamics of all the studied H-bonds.
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20 Lee mas

Hydration of Ca-montmorillonite at basin conditions: A Monte Carlo molecular simulation

Hydration of Ca-montmorillonite at basin conditions: A Monte Carlo molecular simulation

In the present paper is discussed the behavior of Ca- montmorillonite under surface and low-depth environments, as determined from molecular simulations. Reactions on the clay surface are fundamental to establish interrelations with parent minerals and understanding related processes. Molecular simulations allow characterization of the clay interlamellar space at the atomic and molecular levels, identifying fundamental properties, reaction mechanisms, thermodynamics, and kinetics of reactions, mimicking in situ conditions not easily reproduced experimentally or where direct observation is not simple.
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12 Lee mas

Synthesis, Biological Evaluation, and Molecular Simulation of Chalcones and Aurones as Selective MAO B Inhibitors

Synthesis, Biological Evaluation, and Molecular Simulation of Chalcones and Aurones as Selective MAO B Inhibitors

Among the many pharmacologically interesting applications of chalcones, their potential as monoamine oxidase inhibi- tors (MAOi) has been recently described by different groups (23 – 26). MAO is a flavoprotein involved in the degradation of a wide range of endogenous and exogenous monoamines, including the neurotransmitters serotonin, dopamine, and noradrenaline (27). The enzyme exists in two isoforms, MAO-A and MAO-B (28), which are bound to the mitochon- drial outer membrane as dimers (29,30). Both proteins have similar structures and molecular weights (70% amino acid sequence identity), but differ in their selectivity for substrates and inhibitors (27). As MAO-A and MAO-B modulate the lev- els of key signaling molecules, inhibitors of these enzymes have been developed as drugs for the treatment of neuro- psychiatric and neurodegenerative disorders (26). Thus, reversible MAO-A inhibitors such as moclobemide (31) are currently used as effective antidepressants, whereas MAO- B inhibitors are useful in the treatment of Parkinson 0 s dis- ease (26,32). The latter indication is especially relevant in elderly patients with Parkinson 0 s disease, as it has been shown that brain MAO-B levels increase with age, resulting in an acceleration of the neurodegenerative processes (33,34). Therefore, as the detailed chemical structures of MAO-A and MAO-B are available, this information provides new possibilities for the development of promising novel inhibitors (35 – 37).
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11 Lee mas

Application of molecular simulation techniques to the design of nanosystems

Application of molecular simulation techniques to the design of nanosystems

researchers prepared a series of nT dendrimers, where n refers to the number of thiophene rings (T), with n= 3, 6, 7, 14, 15 and 30 using metal-mediated coupling reactions through a convergent approach. The potential use of such dendrimers in optoelectronics and molecular electronics was evidenced by their very broad absorption spectra and the ability of the bigger dendrimers to self-assemble on different solid substrates forming nanowires and 2-D crystalline structures. On the other hand, Bäuerle and co-workers 6 synthesized different all-thiophene dendrimers containing up to 90 thiophene rings (90T) with a divergent/convergent approach to facilitate the inclusion of functionalities in the external surface of the conducting dendrimer. More recently, femtosecond transient absorption measurements showed the suitability of all-thiophene dendrimers as light harvesting antennae for solar cells devices. 7 Concerning their optical properties, non-linear optical and excited state dynamical investigations evidenced a delocalization of the excitation throughout all the thiophene units and ultrafast energy transfer to the longest branch of the dendrimer. 7 Moreover, all-thiophene dendrimers have been demonstrated to be good sensors for entangled photons at very low flux making them suitable materials for imaging of biological systems, quantum optical applications and remote sensing. 9
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313 Lee mas

Molecular Dynamics Simulation of Polymer-Metal Bonds

Molecular Dynamics Simulation of Polymer-Metal Bonds

Molecular simulation is becoming a very powerful tool for studying dynamic phenomena in materials. The simulation yields information about interaction at length and time scales unattainable by experimental mea- surements and unpredictable by continuum theories. This is especially meaningful when referring to bonding between a polymer and a metal substrate. A very important characteristic of polymers is that their physical properties do not rely on the detailed chemical structure of the molecular chains but only on their flexibility, and accordingly they will be able to adopt different conformations. In this paper, a molecular simulation of the bonding between vinyl ester polymer and steel is presented. Four different polymers with increasing chain lengths have been studied. Atomic co-ordinates are adjusted in order to reduce the molecular energy. Conformational changes in the macromolecules have been followed to obtain the polymer pair correlation function. Radius of gyration and end-to-end distance distributions of the individual chains have been used as a quantitative measurement of their flexibility. There exists a correlation between flexibility of the molecular chains and the energy of adhesion between the polymer and the metal substrate. Close contacts between the two materials are established at certain points but every atom up to a certain distance from the interface contributes to the total value of the adhesion energy of the system.
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14 Lee mas

Self Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse Grained Molecular Dynamics Simulation Approach

Self Assembly Behavior of Amphiphilic Janus Dendrimers in Water: A Combined Experimental and Coarse Grained Molecular Dynamics Simulation Approach

In this work, experimental methods and CG-MD simulation were combined to evaluate the self- assembly behavior in water of a second-generation bis-MPA amphiphilic Janus dendrimer (Figure 1). Bis-MPA dendrimers have already been studied [2], being perfectly suitable to build drug carriers, due to their low cytotoxicity and biodegradability. Nevertheless, this is the first report where the self- assembly phenomenon of this type of amphiphilic JD is molecularly explored using a CG-MD simulation. Results obtained by CG-MD simulation agreed with the information collected in the experimental method: both strategies coincide in the formation of assemblies in water, with no interdigitated bilayer membranes. However, differences in particle size and morphology of these assemblies were found. Although these differences, the CG-MD simulation results provide important insights related to the mechanism of formation of the assemblies and dendrimer parameters that are difficult to obtain through experimental methods. This information is relevant for the prediction of supramolecular structure properties of novel JDs with application in the development of drug delivery systems.
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15 Lee mas

CBTC Test Simulation Bench

CBTC Test Simulation Bench

We may state that in spite of the development costs for this type of tool, the cost of track tests is reduced considerably thanks to this simulation environment, since the number of track tests is reduced, thereby reducing the use of infrastructure and rolling stock set aside for this purpose. This cost saving becomes more hidden if it is borne in mind that it is a polyvalent system, as it can be used for any line that implements CBTC.

11 Lee mas

Molecular dynamics simulation of the regrowth of nanometric multigate Si devices

Molecular dynamics simulation of the regrowth of nanometric multigate Si devices

(Received 1 September 2011; accepted 24 December 2011; published online 2 February 2012) We use molecular dynamics (MD) simulation techniques to study the regrowth of nanometric multigate Si devices, such as fins and nanowires, surrounded by free surfaces and interfaces with amorphous material. Our results indicate that atoms in amorphous regions close to lateral free surfaces or interfaces rearrange at a slower rate compared to those in bulk due to the discontinuity of the lateral crystalline template. Consequently, the recrystallization front which advances faster in the device center than at the interfaces adopts new orientations. Regrowth then proceeds depending on the particular orientation of the new amorphous/crystal interfaces. In the particular case of h110i oriented fins, the new amorphous/crystal interfaces are aligned along the h111i direction, which produces frequent twining during further regrowth. Based on our simulation results, we propose alternatives to overcome this defected recrystallization in multigate structures: device orientation along h100i to prevent the formation of limiting {111} amorphous/crystal interfaces and presence of a crystalline seed along the device body to favor regrowth perpendicular to the lateral surfaces/interfaces rather than parallel to them. V C 2012 American Institute of Physics.
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6 Lee mas

Generation of amorphous Si structurally compatible with experimental samples through the quenching process: A systematic molecular dynamics simulation study

Generation of amorphous Si structurally compatible with experimental samples through the quenching process: A systematic molecular dynamics simulation study

sole restriction that each atom must be perfectly coordinated according to its valence. For this purpose, small deviations from the crystalline bond angle and bond length are allowed. Despite the simplicity of this idea, its practical realization is not straightforward. The first algorithm to construct a CRN structure for covalent amorphous materials was developed by Wooten, Winer and Weaire, the so-called WWW algorithm [31]. It starts from the crystalline structure, and it introduces local bond rearrangements in the lattice while keeping the four-fold coordination of Si atoms. Barkema and Mousseau (BM) optimized the WWW algorithm [32, 33] and removed the restriction of starting from a crystalline structure while their algorithm also forces four-fold coordination. Both the WWW and the BM procedures result in a-Si samples where all atoms are four-fold coordinated, and thus satisfying the principle of the CRN model, but intrinsic defects present in experimental samples are not reproduced. Neither the algorithms used in WWW and BM procedures are based on any phys- ical process nor experimental data is used as reference during the generation of the a-Si samples. Nevertheless the pair correlation function (PCF) of generated samples agree very well with experimental results [31–33]. A similar procedure to WWW and BM consists on the accumulation of bond defects in c-Si [34–36]. Bond defects are local rearrangements of bonds in the Si lattice with no excess or deficit of atoms and keeping the four-fold co- ordination of atoms. This defect can result from a pure ballistic process or by incomplete Si interstitial-vacancy recombination, and it has been used for modeling ion-beam-induced amorphization and recrystallization of c-Si [34, 35]. a-Si samples generated by the accumulation of bond defects have large concentration of coordination defects as the desired concentration of bond defects is first introduced in the simulation cell and then the re- sulting configuration is relaxed [36], while in WWW and BM models relaxation is performed after each bond rearrangement.
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21 Lee mas

Microarchitecture simulation for security

Microarchitecture simulation for security

In order to achieve a clean and readable representation, we decided to use the func- tional programming language Haskell to implement the model. The purpose was to be able to simulate the behaviour of the microarchitecture of computers with different characteristics, such as cache replacement policies, size of the cache and associativ- ity. Hence the model had to be parametric. Real-life performance and implementation details that do not affect security are not relevant to the model. Therefore, in order to make the simulation faster, and the mechanisms easier to understand, we decided to make an abstraction of the microarchitecture: instead of modeling all the elements, the model had to simulate the behaviour of the relevant features.
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67 Lee mas

The ATLAS Simulation Infrastructure

The ATLAS Simulation Infrastructure

The last step before using a release for production is physics validation. A dedicated group of experts, including representatives from every detector performance (e.g. track- ing, b-tagging, and jet reconstruction groups) and physics group (e.g. Standard Model, supersymmetry, and exotics search groups) in ATLAS, runs physics analyses on the val- idation samples. Their task is to verify the quality of the single object reconstruction (e.g. jets, electrons, and muons) and the results of more complex physics analyses (e.g. mass reconstruction in Z → μ + μ − , Z → e + e − , and t t ¯ events). The relatively large validation samples may expose minor problems that could not be found with lower statistics, for example a shift of a few percent in the reconstructed en- ergy. In order to properly validate each version of the soft- ware, the results from each release are typically compared to those of previous validated releases. The software must, therefore, maintain backwards-compatibility in order to al- low fair comparisons. Shifts in file format are carefully co- ordinated, and maintenance of the old format is continued for as long as necessary to ensure result consistency. The physics validation procedure is also used for checking major changes in the fast and full simulation (detector description, change in the simulation parameters, etc.).
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52 Lee mas

Essays on simulation methods

Essays on simulation methods

Next, I assessed a Monte Carlo simulation model where demand functions are steeper thus storage plays a greater role and is more frequent. Tables 10 to 18 present the results of the second parameterization (3.1[2]). Results show that small samples bias increases for the Simulation estimators. In particular SMM, IND (M1), EMM (M1), and EMM (M2) tend to underestimate parameters a and b. I observe that IND (M2) underestimate a and over-estimates b while EMM (M3) and EMM (M4), over-estimates a and underestimate b. As the sample size increases, the bias is reduced and for a sample size T = 10000 the average RMSE for all estimates converge to 0.01 for a and 0.03 for b. For small sample, the performance of PML estimator underestimates a and over-estimates b. In general terms, both parameter estimates are more efficient than the Simulation estimators. Yet, as sample size increases parameter a tend to stabilize at 0.94. I observe that although bias might be small compared to CML and UML methods for a sample T = 10000, estimators have substantially better precision where the bias and the RSME converge to almost zero.
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116 Lee mas

Flash mental simulation (2010)

Flash mental simulation (2010)

La FMS se distingue de una hipnosis clásica por la menor profundidad alcanzada en la simulación, del nivel hipnótico a volver casi no hipnótica, la secuencia de operaciones que van cumplidas (aunque se pueda regular bastante fácilmente, la profundidad del estado hipnótico del sujeto: -NdA). Otra diferencia operativa está en el hecho, que en el caso de la utilización de técnicas hipnóticas para liberar el abducido de su situación, estas deben ser antepuestas a oportunas preparaciones del sujeto, a través de coloquios designados a identificar su vivido con la experiencia alienígena y a prepararlo, a través del modelo VAC y de las Anclas, a la sesión hipnótica verdadera. La utilización de la FMS, en cambio, puede ser conducida sin particulares problemáticas pero se recuerda que el sujeto en cambio, después de la aplicación de la simulación mental, va observado seguidamente y todos los días, para darle todos los soportes necesarios, para salir definitivamente de su problema, que se representa a menudo, aunque el sujeto aparece ahora capaz de poderlo gestionar seguramente bien. El apoyo psicológico debe durar por lo menos un mes (de uno a tres meses) después de la aplicación de la flash simulation.
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69 Lee mas

TítuloSexado molecular en la corneja negra ("Corvus corone")

TítuloSexado molecular en la corneja negra ("Corvus corone")

Conocer el sexo de los individuos de una población es fundamental para distintas actividades humanas. En el caso de las aves no ratites, se han desarrollado varios protocolos basados en el gen CHD1 que se encuentra en ambos cromosomas sexuales. En este Trabajo de Fin de Grado se ha procedido al sexado de 58 individuos de Corvus corone pertenecientes a una población de la provincia de León. Cuarenta y siete de las 49 muestras problemas fueron sexadas amplificando dos intrones del gen CHD1 mediante sendas parejas de primers: P2/P8 (Griffiths et al. 1998) y 3007/3112 (Ellegren & Fridolfsson 1997). Como resultado del presente TFG se diseñó un único programa de termociclador que permite simultanear ambas reacciones de amplificación, disminuyendo así el tiempo de procesado en 2,5 horas por muestra. Con motivo de la necesidad de confirmar el sexado de dos muestras problemáticas se incorporó el protocolo de Wang et al. (2010), alternativo al de Griffiths et al. y optimizado para aves Passeriformes. El sexado molecular realizado para el presente TFG ha supuesto un coste aproximado de 8,11 € por muestra. Dicho coste se encuentra dentro del rango de precios ofertados por distintas instituciones españolas (3,9 - 15,75 €/muestra, IVA incluido).
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36 Lee mas

Atmospheric motion vectors from model simulations. Part II: Interpretation as spatial and vertical averages of wind and role of clouds

Atmospheric motion vectors from model simulations. Part II: Interpretation as spatial and vertical averages of wind and role of clouds

detailed description of the entire true atmosphere on a high-resolution grid. Cloud-related variables, such as liquid-water mixing ratio or ice mixing ratio, are either part of the simulation output or can be calculated from it. This fact allows the exploration of alternative inter- pretations of AMVs involving, for example, the vertical location of cloud layers, and also allows one to study how specific conditions of the ambient cloud affect AMV quality. Provided the simulation is realistic, the simula- tion framework allows a more detailed and focused anal- ysis than is normally possible when using real observations. In the current study, we use the possibilities offered by the simulation framework to explore alternative inter- pretations of AMVs as vertical as well as spatial aver- ages and to explore the impact of reassigning AMVs to vertical levels or layers related to the model ambient cloud layer. In particular, we revisit the traditional as- sumption that high-level and low-level AMVs best rep- resent, respectively, the wind at the top and at the base of the ambient cloud layer. The structure of the paper is as follows. Section 2 describes briefly the data used in the study. Section 3 focuses on the interpretation of AMVs as horizontal and vertical averages of wind. Section 4 con- centrates on AMV observation operators that include cloud variables, and section 5 concludes the paper, sum- marizing and pointing at directions for future work.
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18 Lee mas

Molecular dynamics modeling and simulation of void growth in two dimensions

Molecular dynamics modeling and simulation of void growth in two dimensions

The mechanisms of void growth by plastic deformation were studied in a two-dimensional framework by means of molecular dynamics of a 2D periodic voided crystal, in which the circular voids are located at the corners of a square array. To this end, a suitable interatomic potential was adapted to obtain a 2D material whose behavior was in agreement with the standard results for dislocation plasticity in fee metals. In the range of void sizes analyzed (1.5 to 100 nm), it was found that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surfaces. The yield stress, defined as the stress necessary to nucleate stable dislocations, was independent of the void radius except for very small voids (R < 10 nm), in which the reduction in the surface energy density associated to the void surface increased the yield stress. The yield stress and the hardening rate after yielding of the periodic voided crystal decreased with temperature but the void growth rate was not very sensitive to this factor compared with multiaxiality effect. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with the hydrostatic stresses.
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17 Lee mas

Molecular dynamics simulation of the early stages of self interstitial clustering in silicon

Molecular dynamics simulation of the early stages of self interstitial clustering in silicon

We have studied the early stages of self-interstitial clustering in silicon using molecular dynamics simulation techniques. We have generated silicon samples of over 200000 atoms where we introduced a 0.5% extra concentration of self-interstitials. Then samples were annealed at several temperatures. During the simulations we observed the formation of interstitial clusters with different atomic structures, ranging from spherical and amorphous-like clusters, to highly ordered extended configurations such as (110) chains, {111} rod-like defects and dislocation loops, and {100} planar defects. This last type of defects, while common in germanium, have not been observed in silicon until very recently, in ultra-fast laser annealing experiments. The particular morphology of formed interstitial clusters is found to be related to the annealing temperature, as it is observed in the experiments. From the molecular dynamics simulations we have analyzed the atomic mechanisms leading to the formation and growth of interstitial clusters, with special attention to the newly found {100} planar defects.
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6 Lee mas

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