Modelización de los Procesos de Cristalización en Poliolefinas

“Por lo tanto, la cristalización de polímeros se supone, y en las teorías se describe a menudo, como un proceso de múltiples pasos con muchos aspectos físico-químicos y estructurales influyendo en él. Debido a la propia estructura de la cadena, es fácil entender que un proceso que es termodinámicamente forzado a aumentar su ordenamiento local, se vea obstaculizado geométricamente y, por tanto, no puede conducirse a un estado de equilibrio final. Como resultado, se forman habitualmente estructuras de no equilibrio con diferentes características dependiendo de la temperatura, presión, cizallamiento y otros parámetros físico-químicos del sistema”. Estas palabras, pronunciadas recientemente por el profesor Bernhard Wunderlich, uno de los mas relevantes fisico-quimicos que han abordado en las ultimas décadas el estudio del estado físico de las macromoléculas, adelantan lo que de alguna manera se explicita en esta memoria y constituyen el “leitmotiv” de este trabajo de tesis. El mecanismo de la cristalización de polímeros esta aun bajo debate en la comunidad de la física de polímeros y la mayoría de los abordajes experimentales se explican a través de la teoría LH. Esta teoría clásica debida a Lauritzen y Hoffman (LH), y que es una generalización de la teoría de cristalización de una molécula pequeña desde la fase de vapor, describe satisfactoriamente muchas observaciones experimentales aunque esta lejos de explicar el complejo fenómeno de la cristalización de polímeros. De hecho, la formulación original de esta teoría en el National Bureau of Standards, a comienzos de la década de los 70, sufrió varias reformulaciones importantes a lo largo de la década de los 80, buscando su adaptación a los hallazgos experimentales. Así nació el régimen III de cristalización que posibilita la creacion de nichos moleculares en la superficie y que dio pie al paradigma ofrecido por Sadler y col., para justificar los experimentos que se obtenian por “scattering” de neutrones y otras técnicas como la técnica de “droplets” o enfriamiento rapido. Por encima de todo, el gran éxito de la teoría radica en que explica la dependencia inversa entre el tamaño del plegado molecular y el subenfriamiento, definido este ultimo como el intervalo de temperatura que media entre la temperatura de equilibrio y la temperatura de cristalización. El problema concreto que aborda esta tesis es el estudio de los procesos de ordenamiento de poliolefinas con distinto grado de ramificacion mediante simulaciones numéricas. Los copolimeros estudiados en esta tesis se consideran materiales modelo de gran homogeneidad molecular desde el punto de vista de la distribución de tamaños y de ramificaciones en la cadena polimérica. Se eligieron estas poliolefinas debido al gran interes experimental en conocer el cambio en las propiedades fisicas de los materiales dependiendo del tipo y cantidad de comonomero utilizado. Además, son modelos sobre los que existen una ingente cantidad de información experimental, que es algo que preocupa siempre al crear una realidad virtual como es la simulación. La experiencia en el grupo Biophym es que los resultados de simulación deben de tener siempre un correlato mas o menos próximo experimental y ese argumento se maneja a lo largo de esta memoria. Empíricamente, se conoce muy bien que las propiedades físicas de las poliolefinas, en suma dependen del tipo y de la cantidad de ramificaciones que presenta el material polimérico. Sin embargo, tal como se ha explicado no existen modelos teóricos adecuados que expliquen los mecanismos subyacentes de los efectos de las ramas. La memoria de este trabajo es amplia por la complejidad del tema. Se inicia con una extensa introducción sobre los conceptos básicos de una macromolecula que son relevantes para entender el contenido del resto de la memoria. Se definen los conceptos de macromolecula flexible, distribuciones y momentos, y su comportamiento en disolución y fundido con los correspondientes parametros caracteristicos. Se pone especial énfasis en el concepto de “entanglement” o enmaranamiento por considerarse clave a la hora de tratar macromoléculas con una longitud superior a la longitud critica de enmaranamiento. Finaliza esta introducción con una reseña sobre el estado del arte en la simulación de los procesos de cristalización. En un segundo capitulo del trabajo se expone detalladamente la metodología usada en cada grupo de casos. En el primer capitulo de resultados, se discuten los estudios de simulación en disolución diluida para sistemas lineales y ramificados de cadena única. Este caso mas simple depende claramente del potencial de torsión elegido tal como se discute a lo largo del texto. La formación de los núcleos “babys” propuestos por Muthukumar parece que son consecuencia del potencial de torsión, ya que este facilita los estados de torsión mas estables. Así que se propone el análisis de otros potenciales que son igualmente utilizados y los resultados obtenidos sobre la cristalización, discutidos en consecuencia. Seguidamente, en un segundo capitulo de resultados se estudian moleculas de alcanos de cadena larga lineales y ramificados en un fundido por simulaciones atomisticas como un modelo de polietileno. Los resultados atomisticos pese a ser de gran detalle no logran captar en su totalidad los efectos experimentales que se observan en los fundidos subenfriados en su etapa previa al estado ordenado. Por esta razon se discuten en los capítulos 3 y 4 de resultados sistemas de cadenas cortas y largas utilizando dos modelos de grano grueso (CG-PVA y CG-PE). El modelo CG-PE se desarrollo durante la tesis. El uso de modelos de grano grueso garantiza una mayor eficiencia computacional con respecto a los modelos atomísticos y son suficientes para mostrar los fenómenos a la escala relevante para la cristalización. En todos estos estudios mencionados se sigue la evolución de los procesos de ordenamiento y de fusión en simulaciones de relajación isoterma y no isoterma. Como resultado de los modelos de simulación, se han evaluado distintas propiedades fisicas como la longitud de segmento ordenado, la cristalinidad, temperaturas de fusion/cristalizacion, etc., lo que permite una comparación con los resultados experimentales. Se demuestra claramente que los sistemas ramificados retrasan y dificultan el orden de la cadena polimérica y por tanto, las regiones cristalinas ordenadas decrecen al crecer las ramas. Como una conclusión general parece mostrarse una tendencia a la formación de estructuras localmente ordenadas que crecen como bloques para completar el espacio de cristalización que puede alcanzarse a una temperatura y a una escala de tiempo determinada. Finalmente hay que señalar que los efectos observados, estan en concordancia con otros resultados tanto teoricos/simulacion como experimentales discutidos a lo largo de esta memoria. Su resumen se muestra en un capitulo de conclusiones y líneas futuras de investigación que se abren como consecuencia de esta memoria. Hay que mencionar que el ritmo de investigación se ha acentuado notablemente en el ultimo ano de trabajo, en parte debido a las ventajas notables obtenidas por el uso de la metodología de grano grueso que pese a ser muy importante para esta memoria no repercute fácilmente en trabajos publicables. Todo ello justifica que gran parte de los resultados esten en fase de publicación. Abstract “Polymer crystallization is therefore assumed, and in theories often described, to be a multi step process with many influencing aspects. Because of the chain structure, it is easy to understand that a process which is thermodynamically forced to increase local ordering but is geometrically hindered cannot proceed into a final equilibrium state. As a result, nonequilibrium structures with different characteristics are usually formed, which depend on temperature, pressure, shearing and other parameters”. These words, recently written by Professor Bernhard Wunderlich, one of the most prominent researchers in polymer physics, put somehow in value the "leitmotiv "of this thesis. The crystallization mechanism of polymers is still under debate in the physics community and most of the experimental findings are still explained by invoking the LH theory. This classical theory, which was initially formulated by Lauritzen and Hoffman (LH), is indeed a generalization of the crystallization theory for small molecules from the vapor phase. Even though it describes satisfactorily many experimental observations, it is far from explaining the complex phenomenon of polymer crystallization. This theory was firstly devised in the early 70s at the National Bureau of Standards. It was successively reformulated along the 80s to fit the experimental findings. Thus, the crystallization regime III was introduced into the theory in order to explain the results found in neutron scattering, droplet or quenching experiments. This concept defines the roughness of the crystallization surface leading to the paradigm proposed by Sadler et al. The great success of this theory is the ability to explain the inverse dependence of the molecular folding size on the supercooling, the latter defined as the temperature interval between the equilibrium temperature and the crystallization temperature. The main scope of this thesis is the study of ordering processes in polyolefins with different degree of branching by using computer simulations. The copolymers studied along this work are considered materials of high molecular homogeneity, from the point of view of both size and branching distributions of the polymer chain. These polyolefins were selected due to the great interest to understand their structure– property relationships. It is important to note that there is a vast amount of experimental data concerning these materials, which is essential to create a virtual reality as is the simulation. The Biophym research group has a wide experience in the correlation between simulation data and experimental results, being this idea highly alive along this work. Empirically, it is well-known that the physical properties of the polyolefins depend on the type and amount of branches presented in the polymeric material. However, there are not suitable models to explain the underlying mechanisms associated to branching. This report is extensive due to the complexity of the topic under study. It begins with a general introduction to the basics concepts of macromolecular physics. This chapter is relevant to understand the content of the present document. Some concepts are defined along this section, among others the flexibility of macromolecules, size distributions and moments, and the behavior in solution and melt along with their corresponding characteristic parameters. Special emphasis is placed on the concept of "entanglement" which is a key item when dealing with macromolecules having a molecular size greater than the critical entanglement length. The introduction finishes with a review of the state of art on the simulation of crystallization processes. The second chapter of the thesis describes, in detail, the computational methodology used in each study. In the first results section, we discuss the simulation studies in dilute solution for linear and short chain branched single chain models. The simplest case is clearly dependent on the selected torsion potential as it is discussed throughout the text. For example, the formation of baby nuclei proposed by Mutukhumar seems to result from the effects of the torsion potential. Thus, we propose the analysis of other torsion potentials that are also used by other research groups. The results obtained on crystallization processes are accordingly discussed. Then, in a second results section, we study linear and branched long-chain alkane molecules in a melt by atomistic simulations as a polyethylene-like model. In spite of the great detail given by atomistic simulations, they are not able to fully capture the experimental facts observed in supercooled melts, in particular the pre-ordered states. For this reason, we discuss short and long chains systems using two coarse-grained models (CG-PVA and CG-PE) in section 3 and 4 of chapter 2. The CG-PE model was developed during the thesis. The use of coarse-grained models ensures greater computational efficiency with respect to atomistic models and is enough to show the relevant scale phenomena for crystallization. In all the analysis we follow the evolution of the ordering and melting processes by both isothermal and non isothermal simulations. During this thesis we have obtained different physical properties such as stem length, crystallinity, melting/crystallization temperatures, and so on. We show that branches in the chains cause a delay in the crystallization and hinder the ordering of the polymer chain. Therefore, crystalline regions decrease in size as branching increases. As a general conclusion, it seems that there is a tendency in the macromolecular systems to form ordered structures, which can grown locally as blocks, occupying the crystallization space at a given temperature and time scale. Finally it should be noted that the observed effects are consistent with both, other theoretical/simulation and experimental results. The summary is provided in the conclusions chapter along with future research lines that open as result of this report. It should be mentioned that the research work has speeded up markedly in the last year, in part because of the remarkable benefits obtained by the use of coarse-grained methodology that despite being very important for this thesis work, is not easily publishable by itself. All this justify that most of the results are still in the publication phase.

Towards the automatic generation of card games through Grammar-Guided Genetic Programming

We demonstrate generating complete and playable card games using evolutionary algorithms. Card games are represented in a previously devised card game description language, a context-free grammar. The syntax of this language allows us to use grammar-guided genetic programming. Candidate card games are evaluated through a cascading evaluation function, a multi-step process where games with undesired properties are progressively weeded out. Three representa- tive examples of generated games are analysed. We observed that these games are reasonably balanced and have skill ele- ments, they are not yet entertaining for human players. The particular shortcomings of the examples are discussed in re- gard to the generative process to be able to generate quality games

Bounded non-deterministic planning for multimedia adaptation

This paper proposes a novel combination of artificial intelligence planning and other techniques for improving decision-making in the context of multi-step multimedia content adaptation. In particular, it describes a method that allows decision-making (selecting the adaptation to perform) in situations where third-party pluggable multimedia conversion modules are involved and the multimedia adaptation planner does not know their exact adaptation capabilities. In this approach, the multimedia adaptation planner module is only responsible for a part of the required decisions; the pluggable modules make additional decisions based on different criteria. We demonstrate that partial decision-making is not only attainable, but also introduces advantages with respect to a system in which these conversion modules are not capable of providing additional decisions. This means that transferring decisions from the multi-step multimedia adaptation planner to the pluggable conversion modules increases the flexibility of the adaptation. Moreover, by allowing conversion modules to be only partially described, the range of problems that these modules can address increases, while significantly decreasing both the description length of the adaptation capabilities and the planning decision time. Finally, we specify the conditions under which knowing the partial adaptation capabilities of a set of conversion modules will be enough to compute a proper adaptation plan.

Molecular evolution of breast cancer

Molecular analysis of invasive breast cancer and its precursors has furthered our understanding of breast cancer progression. In the past few years, new multi-step pathways of breast cancer progression have been delineated through genotypic-phenotypic correlations. Nuclear grade, more than any other pathological feature, is strongly associated with the number and pattern of molecular genetic abnormalities in breast cancer cells. Thus, there are two distinct major pathways to the evolution of low- and high-grade invasive carcinomas: whilst the former consistently show oestrogen receptor (ER) and progesterone receptor (PgR) positivity and 16q loss, the latter are usually ER/PgR-negative and show Her-2 over-expression/amplification and complex karyotypes. The boundaries between the evolutionary pathways of well-differentiated/low-grade ductal and lobular carcinomas have been blurred, with changes in E-cadherin expression being one of the few distinguishing features between the two. In addition, lesions long thought to be precursors of breast carcinomas, such as hyperplasia of usual type, are currently considered mere risk indicators, whilst columnar cell lesions are now implicated as non-obligate precursors of atypical ductal hyperplasia (ADH) and well-differentiated ductal carcinoma in situ (DCIS). However, only through the combination of comprehensive morphological analysis and cutting-edge molecular tools can this knowledge be translated into clinical practice and patient management. Copyright (C) 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley Sons, Ltd.

A new approach to the synthesis of nanocrystal conjugated polymer composites

A novel one pot process has been developed for the preparation of PbS nanocrystals in the conjugated polymer poly 2-methoxy,5-(2 ethyl-hexyloxy-p-phenylenevinylene) (MEH-PPV). Current techniques for making such composite materials rely upon synthesizing the nanocrystals and conducting polymer separately, and subsequently mixing them. This multi-step technique has two serious drawbacks: templating surfactant must be removed before mixing, and co-solvent incompatibility causes aggregation. In our method, we eliminate the need for an initial surfactant by using the conducting polymer to terminate and template nanocrystal growth. Additionally, the final product is soluble in a single solvent. We present materials analysis which shows PbS nanocrystals can be grown directly in a conducting polymer, the resulting composite is highly ordered and nanocrystal size can be controlled.

Efficiently computing weighted proximity relationships in spatial databases

Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. In this paper, we investigate the problem of evaluating the top k distinguished “features” for a “cluster” based on weighted proximity relationships between the cluster and features. We measure proximity in an average fashion to address possible nonuniform data distribution in a cluster. Combining a standard multi-step paradigm with new lower and upper proximity bounds, we presented an efficient algorithm to solve the problem. The algorithm is implemented in several different modes. Our experiment results not only give a comparison among them but also illustrate the efficiency of the algorithm.

Tuneable compensator of dispersion and slope using non-uniformly strained chirped fibre grating

Summary form only given. A novel method for tuning the second and the third order dispersion using a simple multi-point bending device has been demonstrated. A simple model has been developed that allows to calculate the exact bending profile required for compensation for the given values of dispersion and dispersion slope.

Pryolytic and kinetic study of Chlorella Vulgaris under isothermal and non-isothermal conditions

Algae are a new potential biomass for energy production but there is limited information on their pyrolysis and kinetics. The main aim of this thesis is to investigate the pyrolytic behaviour and kinetics of Chlorella vulgaris, a green microalga. Under pyrolysis conditions, these microalgae show their comparable capabilities to terrestrial biomass for energy and chemicals production. Also, the evidence from a preliminary pyrolysis by the intermediate pilot-scale reactor supports the applicability of these microalgae in the existing pyrolysis reactor. Thermal decomposition of Chlorella vulgaris occurs in a wide range of temperature (200-550°C) with multi-step reactions. To evaluate the kinetic parameters of their pyrolysis process, two approaches which are isothermal and non-isothermal experiments are applied in this work. New developed Pyrolysis-Mass Spectrometry (Py-MS) technique has the potential for isothermal measurements with a short run time and small sample size requirement. The equipment and procedure are assessed by the kinetic evaluation of thermal decomposition of polyethylene and lignocellulosic derived materials (cellulose, hemicellulose, and lignin). In the case of non-isothermal experiment, Thermogravimetry- Mass Spectrometry (TG-MS) technique is used in this work. Evolved gas analysis provides the information on the evolution of volatiles and these data lead to a multi-component model. Triplet kinetic values (apparent activation energy, pre-exponential factor, and apparent reaction order) from isothermal experiment are 57 (kJ/mol), 5.32 (logA, min-1), 1.21-1.45; 9 (kJ/mol), 1.75 (logA, min-1), 1.45 and 40 (kJ/mol), 3.88 (logA, min-1), 1.45- 1.15 for low, middle and high temperature region, respectively. The kinetic parameters from non-isothermal experiment are varied depending on the different fractions in algal biomass when the range of apparent activation energies are 73-207 (kJ/mol); pre-exponential factor are 5-16 (logA, min-1); and apparent reaction orders are 1.32–2.00. The kinetic procedures reported in this thesis are able to be applied to other kinds of biomass and algae for future works.

Techno-economic assessment and uncertainty analysis of thermochemical processes for second generation biofuels

Biomass-To-Liquid (BTL) is one of the most promising low carbon processes available to support the expanding transportation sector. This multi-step process produces hydrocarbon fuels from biomass, the so-called “second generation biofuels” that, unlike first generation biofuels, have the ability to make use of a wider range of biomass feedstock than just plant oils and sugar/starch components. A BTL process based on gasification has yet to be commercialized. This work focuses on the techno-economic feasibility of nine BTL plants. The scope was limited to hydrocarbon products as these can be readily incorporated and integrated into conventional markets and supply chains. The evaluated BTL systems were based on pressurised oxygen gasification of wood biomass or bio-oil and they were characterised by different fuel synthesis processes including: Fischer-Tropsch synthesis, the Methanol to Gasoline (MTG) process and the Topsoe Integrated Gasoline (TIGAS) synthesis. This was the first time that these three fuel synthesis technologies were compared in a single, consistent evaluation. The selected process concepts were modelled using the process simulation software IPSEpro to determine mass balances, energy balances and product distributions. For each BTL concept, a cost model was developed in MS Excel to estimate capital, operating and production costs. An uncertainty analysis based on the Monte Carlo statistical method, was also carried out to examine how the uncertainty in the input parameters of the cost model could affect the output (i.e. production cost) of the model. This was the first time that an uncertainty analysis was included in a published techno-economic assessment study of BTL systems. It was found that bio-oil gasification cannot currently compete with solid biomass gasification due to the lower efficiencies and higher costs associated with the additional thermal conversion step of fast pyrolysis. Fischer-Tropsch synthesis was the most promising fuel synthesis technology for commercial production of liquid hydrocarbon fuels since it achieved higher efficiencies and lower costs than TIGAS and MTG. None of the BTL systems were competitive with conventional fossil fuel plants. However, if government tax take was reduced by approximately 33% or a subsidy of £55/t dry biomass was available, transport biofuels could be competitive with conventional fuels. Large scale biofuel production may be possible in the long term through subsidies, fuels price rises and legislation.

Tuneable compensator of dispersion and slope using non-uniformly strained chirped fibre grating

Summary form only given. A novel method for tuning the second and the third order dispersion using a simple multi-point bending device has been demonstrated. A simple model has been developed that allows to calculate the exact bending profile required for compensation for the given values of dispersion and dispersion slope.

Coupling of Heck and hydrogenation reactions in a continuous compact reactor

A continuous multi-step synthesis of 1,2-diphenylethane was performed sequentially in a structured compact reactor. This process involved a Heck C-C coupling reaction followed by the addition of hydrogen to perform reduction of the intermediate obtained in the first step. Both of the reactions were catalysed by microspherical carbon-supported Pd catalysts. Due to the integration of the micro-heat exchanger, the static mixer and the mesoscale packed-bed reaction channel, the compact reactor was proven to be an intensified tool for promoting the reactions. In comparison with the batch reactor, this flow process in the compact reactor was more efficient as: (i) the reaction time was significantly reduced (ca. 7 min versus several hours), (ii) no additional ligands were used and (iii) the reaction was run at lower operational pressure and temperature. Pd leached in the Heck reaction step was shown to be effectively recovered in the following hydrogenation reaction section and the catalytic activity of the system can be mostly retained by reverse flow operation. © 2009 Elsevier Inc. All rights reserved.

Class I T-cell epitope prediction:improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding

Cleavage by the proteasome is responsible for generating the C terminus of T-cell epitopes. Modeling the process of proteasome cleavage as part of a multi-step algorithm for T-cell epitope prediction will reduce the number of non-binders and increase the overall accuracy of the predictive algorithm. Quantitative matrix-based models for prediction of the proteasome cleavage sites in a protein were developed using a training set of 489 naturally processed T-cell epitopes (nonamer peptides) associated with HLA-A and HLA-B molecules. The models were validated using an external test set of 227 T-cell epitopes. The performance of the models was good, identifying 76% of the C-termini correctly. The best model of proteasome cleavage was incorporated as the first step in a three-step algorithm for T-cell epitope prediction, where subsequent steps predicted TAP affinity and MHC binding using previously derived models.

EpiJen:a server for multistep T cell epitope prediction

Background - The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. Results - To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. Conclusion - EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction.

Nonlinear inverse synthesis for high spectral efficiency transmission in optical fibers

In linear communication channels, spectral components (modes) defined by the Fourier transform of the signal propagate without interactions with each other. In certain nonlinear channels, such as the one modelled by the classical nonlinear Schrödinger equation, there are nonlinear modes (nonlinear signal spectrum) that also propagate without interacting with each other and without corresponding nonlinear cross talk, effectively, in a linear manner. Here, we describe in a constructive way how to introduce such nonlinear modes for a given input signal. We investigate the performance of the nonlinear inverse synthesis (NIS) method, in which the information is encoded directly onto the continuous part of the nonlinear signal spectrum. This transmission technique, combined with the appropriate distributed Raman amplification, can provide an effective eigenvalue division multiplexing with high spectral efficiency, thanks to highly suppressed channel cross talk. The proposed NIS approach can be integrated with any modulation formats. Here, we demonstrate numerically the feasibility of merging the NIS technique in a burst mode with high spectral efficiency methods, such as orthogonal frequency division multiplexing and Nyquist pulse shaping with advanced modulation formats (e.g., QPSK, 16QAM, and 64QAM), showing a performance improvement up to 4.5 dB, which is comparable to results achievable with multi-step per span digital back propagation.