京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21123号 / 工博第4487号 / 新制||工||1697(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 佐藤 啓文, 教授 関 修平, 教授 山本 量一 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

The flow properties of polydimethylsiloxane (PDMS) melts at room temperature were studied by measurement of lubrication forces using an Atomic Force Microscopy (AFM) colloidal force probe. A glass probe was driven toward a glass plate at piezo drive rates in the range of 12 – 120 μm/s, which produced shear rates up to ~10⁴ s⁻¹. The forces on the probe and the separation from the plate were measured. Two hypotheses were examined: (1) when a hydrophilic glass is immersed in a flow of polymer melt, does a thin layer of water form at the glass surface to lubricate the flow of polymer and (2) when a polymer melt is subject under a shear stress, do molecules within the melt spatially redistribute to form a lubrication layer of smaller molecules at the solid surface to enhance the flow? To examine the effect of a water lubrication layer, forces were compared in the presence and the absence of a thin water layer. The presence of the water layer was controlled by hydrophobization of the solid. In the second part, the possibility of forming a lubrication layer during shear was examined. Three polymer melts were compared: octamethyltrisiloxane (OMTS, n = 3), PDMS (n _avg = 322), and a mixture of 70 weight% PDMS and 30 weight% OMTS. We examined whether the spatial variation in the composition of the polymer melt would occur to relieve the shear stress. The prediction was that the trimer (OMTS) would become concentrated in the high shear stress region in the thin film, thereby decreasing the viscosity in that region, and mitigating the shear stress. / Master of Science

The thesis involves computer simulation and theoretical studies of phase transition in soft-condensed matter systems and theoretical understanding of enzyme kinetics along with kinetic proofreading of tRNA-aminoacylation in biological systems. Based on the system and phenomena of interest, the work has be classified into the following four major parts: I. Surface phenomena and surface energy of vapor-liquid interface. II. Condensation of vapor in two and three dimensions. III. Liquid-solid phase transition in polydisperse systems. IV. Enzyme catalysis and kinetic proofreading in biosynthesis. Above mentioned four parts have further been divided into thirteen chapters. In the following we provide a brief chapter-wise outline of the thesis. Part I deals with surface tension and interfacial properties of vapor-liquid interface for Lennard-Jones (LJ) fluid in both two and three dimensions. In Chapter 1, we provide a brief overview of vapor-liquid interface and existing theoretical and computer simulation studies of surface/line tension. In this chapter we also discuss about the existing experimental studies. In Chapter 2, we present computer simulation studies of surface tension in two dimensional Lennard-Jones system. The sensitivity of line tension on range (potential cut-off) of interparticle interaction is discussed in this chapter. We present Density Functional Theory (DFT) of line tension of vapor-liquid interface based on Weeks-Chandler-Anderson (WCA) and Barker-Hendersen (BH) perturbation techniques. We compare the DFT prediction with the computer simulation results. In general, WCA approach has been found to be successful for 3D system in predicting the surface tension. In 2D, however, it does not give good agreement either for phase diagram or for the line tension. In fact, BH also does not give accurate values of the coexistence parameters, however, it predicts better line tension compared to WCA. In Chapter 3 we present both theoretical and computer simulation studies of gas-liquid surface tension for three dimensional Lennard-Jones fluid. We perform non-equilibrium computer simulation study following Transition Matrix Monte Carlo (TMMC) method to obtain surface tension for various ranges of potential and introduce a new scaling relation of surface tension in order to capture both the temperature and interparticle interaction range dependence. The scaling shows excellent agreement with the simulation result and it can also predict the critical temperature with sufficient accuracy. The width of the gas-liquid interface is found to be insensitive to the range of the potential, whereas the density separation of the bulk vapor and liquid phases increases with increasing range of potential. Thus, the major contribution comes from the increasing density separation of the bulk vapor and liquid phases. Part II consists of four chapters, where we focus on the age old problem of nucleation, from the perspective of thermodynamics and kinetics. We account for the rich history of the problem in the introductory Chapter 4. In this chapter we describe various types and examples of the nucleation phenomena, and a brief account of the major theoretical approaches used so far. We begin with the most successful Classical Nucleation Theory (CNT), and then move on to more recent applications of Density Functional Theory (DFT) and other mean-field types of models. We present various experimental techniques used in the literature to obtain rate of nucleation. We conclude with a comparison between the experiments, theories and computational studies. In the next chapter (Chapter 5) we attempt to understand the mechanism of the gas-liquid nucleation in three dimension at large metastability from microscopic point of view. Here we study the nature of sequential growth of all liquid-like clusters (not just the largest cluster) at different degrees of metastability. Therefore, we have ordered the clusters according to their decreasing sizes and identified them in terms of kth largest cluster where, k = 1 denotes the largest cluster in the system, k = 2 represents the second largest and k = 3 is the third largest and so on. We have studied both the free energies and the trajectories of the liquid-like clusters in this extended set of order parameters. We further define Fkl(n) as the free energy of the kth largest cluster with size n. Classical nucleation theory provides an expression of unconditional free energy of a single cluster, F (n) (the free energy of formation of a cluster of size n), which is an intensive property of the system. The study of our conditional free energy surfaces, Fkl(n), reveals a more detailed, microscopic picture of the system’s cluster size distribution that is necessary to understand the kinetics of nucleation and growth at large metastability. The rate of nucleation shows a cross over at kinetic spinodal (the limit of metastability, ∆F1 l = 0). Below kinetic spinodal only one (largest) cluster crosses the critical size through activation whereas above this point more than one cluster grow simultaneously through barrierless diffusion. We present a theoretical analysis of the free energy of kth largest cluster based on order statistics. The theoretical predictions are in excellent agreement with computer simulation results for the range of supersaturation we studied. While the previous chapter focuses on relatively well-studied nucleation mechanism in 3dimensional (3D) LJ system at large metastability, in Chapter 6 we present our studies on the characteristics of the nucleation phenomena in two dimensional Lennard-Jones fluid for different ranges of interparticle interaction. Using various Monte Carlo (MC) methods, we calculate the free energy barrier of nucleation and bulk densities of equilibrium liquid and vapor phases, and also investigate the size and shape of the critical nuclei. We find an interesting interplay between the range of interaction potential and the extent of metastability. The free energy barrier of nucleation strongly depends on the range of interaction potential. The study is carried out at an intermediate level of supersaturation (away from the kinetic spinodal limit). A surprisingly large cutoff (rc � 7.0�, where � is the diameter of LJ particles) in the truncation of the LJ potential is required to obtain converged results. A lower cutoff leads to a substantial deviation in the values of the nucleation barrier, and characteristics of the critical cluster (with respect to full range of interaction). We observe that in 2D system CNT fails to provide a reliable estimate of the free energy barrier. While it is known to slightly overestimate the nucleation barrier in 3D, it underestimates the barrier by � 50% at the saturation ratio S =1.1 (defined as S = P/Pc, where Pc is the coexistence pressure) and at the reduced temperature T � =0.427 (defined as T � = kBT/�, where � is the depth of the potential well). The reason for the marked inadequacy of the CNT in 2D can be attributed to the non-circular nature of the critical clusters. Although the shape becomes increasingly circular and the clusters become more compact with increase in cutoff radius, an appreciable non-circular nature remains even for full potential (without truncation) to make the predictions of CNT inaccurate. In Chapter 7 we report the computer simulation study of nucleation in three dimensional LJ system. At a fixed supersaturation the free energy barrier of nucleation increases with increasing range of interparticle interaction. On increasing range of intermolecular interaction, the kinetic spinodal where the mechanism of nucleation changes from activated barrier crossing to barrierless diffusion, shifts towards the deep metastable region. Both the critical cluster size and pre-critical minimum in the free energy surface of kth largest cluster shift towards the smaller size at their respective kinetic spinodal as we increase the range of potential. We find only a weak non-trivial (other than supersaturation and surface tension) contribution to the free energy barrier of nucleation. Part III consists of two chapters and focuses on the liquid-solid phase transition of polydisperse fluid. In Chapter 8 we introduce polydisperse systems and their classification based on different identities. We describe the importance and abundance of polydisperse system in nature. The theoretical modeling of different polydisperse systems and their extent of applicability have also been presented. We have discussed about the various factors which control the phase diagram and various phenomena related to the structure and phase transition. In Chapter 9 we present computer simulation study on freezing/melting of Lennard-Jones (LJ) fluid at different polydispersities. The freezing/melting of polydisperse LJ fluids presents an interesting case study, because, as the polydispersity increases the energy-entropy balance becomes increasingly unfavorable for the solid to exist as a stable phase. The energy of the solid increases due to build up of strain energy because of increasing mismatch in size of the neighbors, while the entropy of the liquid increases. These two factors lead to the existence of a terminal polydispersity. We find beyond the terminal ploydispersity, δ. 0.11system remains in the disorder state even at very high pressure and low temperature. The terminal polydispersity obtained in the present study is close to the experimental value (δt. ≈ 12%). Interestingly, contrary to hard sphere polydisperse fluid, LJ fluid does not exhibit reentrant melting. The last part (Part IV) of the thesis consists of three chapters that deal with the enzyme catalysis and kinetic proofreading of tRNA-aminoacyl synthetases. In Chapter 10 we describe protein synthesis process in biological system and corresponding two processes: aminoacylation of tRNA and translation of amino acid in ribosome. Our interest is to understand the enzyme catalysis involved in aminoacylation of tRNA in the process of protein synthesis. We present the classification of 20 aminoacyl-tRNA synthetases into two classes based on their structure and mode of binding to ATP and tRNA. We discuss all the steps involved in whole tRNA-aminoacylation process. Then we introduce kinetic proofreading during aminoacylation reaction. In Chapter 11 we theoretically analyze the single turn over and steady state reaction mechanism of two classes of aminoacyl-tRNA synthetases. Class I enzymes not only differ in their structure but they also differ with respect to the pre-steady kinetics compared to class II enzymes. We find that the strong binding of product to class I enzymes causes the product release step to be rate limiting step leading to the burst of product formation in pre-steady reaction. On the other hand class II enzymes do not show any burst kinetics. The present study based on time dependent probability statistics is successful in explaining all the experimental results quantitatively. In Chapter 12 we present an augmented kinetic scheme and then employ methods of time dependent probability statistics to understand the mechanism of kinetic proofreading of isoleucyl-tRNA synthetase (IRS) which belongs to class I. We investigate that the enhanced hydrolysis of wrong substrate (Val) enables IRS to discriminate the correct substrate (Ile) and wrong substrate (Val) efficiently. It has been observed that an extra CP1 editing domain serves as an activating domain towards enhanced hydrolysis of Val. The present study is able to explain most of the existing experimental observations. In the concluding note, Chapter 13 lists a few relevant problems that may prove worthwhile to be addressed in future. In the Appendices, we present two of the techniques used in our present computer simulation and theoretical studies. Appendix A describes Grand Canonical Transition Matrix Monte Carlo (GC-TMMC) method which is employed in computer simulation studies of nucleation and surface tension. In Appendix B we present the probabilistic method of waiting time distribution computation used in enzyme catalysis and kinetic proofreading.

La plupart des modules photovolta¨ıques produits sont `a base de silicium.L’efficacit´e de ces modules d´epend fortement de la qualit´e cristalline du siliciumutilis´ee ainsi que de la quantit´e d’impuret´es pr´esente dans le lingotd’origine d’o`u sont issus les modules. Les lingots de silicium sont obtenus aucours d’un proc´ed´e de solidification, durant lequel les impuret´es sont extraitespar ph´enom`ene de s´egr´egation. Le processus de s´egr´egation est influenc´e parl’´ecoulement dans le liquide durant l’´etape de solidification. L’utilisation d’unchamp magn´etique externe permet le contrˆole de l’´ecoulement dans le bainliquide. Dans cette ´etude, l’effet d’un ´ecoulement forc´e sur le processus des´egr´egation est ´etudi´e. Pour cela un dispositif exp´erimental (VB2) et unmod`ele num´erique ont ´et´e d´evelopp´es dans le but de comprendre le rˆole del’´ecoulement sur la forme de l’interface et sur la s´egr´egation des impuret´es. / The photovoltaic modules are generally produced using silicon wafers. Theirelectrical efficiency is related to the crystal quality, which is influenced bythe presence of pollutants in the ingots from which the wafers are cut. Siliconingots are obtained as a result of solidification processes, which implygrowing a crystal from melt. During this solidification process, impurities areseparated from the silicon. The segregation process is greatly influenced bythe melt velocity during the solidification process. The control of the meltflow during the crystallization process can be achieved using external magneticfields. This thesis presents the results of the study on the influence ofthe forced convection induced by a travelling magnetic field (TMF) duringthe solidification process, using both an experimental set-up (VB2) and anumerical model.

The Onsager heat of transport for p-tert-butyltoluene was measured, as part of a series of preliminary experiments towards the determination of the importance of temperature gradients on the air-sea flux of carbon dioxide. The results presented in this thesis imply that the temperature gradient is a major contributor to the magnitude of the air-sea flux. The heat of transport has been measured for the p-tert-butyltoluene system by measuring stationary-state pressure changes for known temperature differences on the vapour side of the interface. At the pressure ranges used the number of mean free paths was always outside the Knudsen zone, but the values of Q* were approximately 100 % of the latent heat of vaporisation. Departures from linearity of plots of P against ΔT are attributed to temperature jumps at the surface of the dry upper plate. Both the results taken for p-tert-butyltoluene and the earlier results for water from this laboratory fit to a Type III BET isotherm, where the c parameter is not constant. They also reveal the importance of the temperature gradient in determining the value of the thermal accommodation coefficient, and provide a new method of measuring thermal accommodation coefficients for a variety of surfaces and vapours

Ce travail est consacré à l'étude expérimentale des écoulements diphasiques et triphasiques d'inclusions (bulles, gouttes, sphères) en milieux tant newtoniens que non newtoniens à l'échelle microscopique et mésoscopique, en utilisant la visualisation par une caméra rapide, la vélocimétrie par images des particules (PIV) ainsi que la micro-vélocimétrie par images des particules. Des bulles et des gouttes ont été étudiées expérimentalement depuis leur formation, en passant par leur déformation jusqu'à leur coalescence. La formation de bulles dans des micro-mélangeurs a été étudiée et caractérisée par l'obtention de champs de vitesses. Différents paramètres, tels que le cisaillement, la géométrie de la zone de formation, les débits ou encore les propriétés physiques ont été testés afin de développer des lois d'échelles. La traversée d'une interface liquide-liquide par une inclusion a été abordée par des expériences originales, permettant de décrire la dynamique du phénomène, de définir des nombres adimensionnels et de mettre en évidence des instabilités interfaciales. L'effet Weissenberg a également été étudié aux différentes échelles afin de comprendre les phénomènes conduisant à son amplification. Enfin, en milieu viscoélastique et rhéofluidifiant, nous avons caractérisé l'écoulement autour d'une inclusion isolée solide par l'obtention de champs de vitesses. Ces résultats ont permis de confirmer l'origine viscoélastique du sillage négatif et de prédire ses caractéristiques / The present work was devoted to the experimental study of the multiphase flow around inclusions in both Newtonian and non-Newtonian media at respectively microscopic and mesoscopic scales, by means of the Particle Image Velocimetry (both PIV and µ-PIV) and fast camera visualization. Bubbles and drops were experimentally studied starting from their formation, the rising and up to their coalescence and fragmentation. Bubble formation in micro-mixers was also investigated and characterized by measuring the liquid velocity fields. Different parameters, such as the shear rate, the geometry of the micro-mixer, the flow rates or the physical properties were tested to develop correlations of power-law kind. The deformation of a liquid-liquid interface due to the passage of an inclusion was investigated by original experiments in order to observe and describe the dynamics of the phenomenon, to define the reliable dimensionless numbers and also to highlight several interfacial instabilities. The Weissenberg effect was also studied at different scales in various non-Newtonian fluids in comparison with Newtonian fluids to understand the amplification phenomena under the combining effects of instability and normal forces. Finally, the flow around an isolated solid inclusion was characterized by performing the measurements of velocity fields in viscoelastic and shear-thinning fluids. These results were used to confirm the viscoelastic origin of the negative wake behind the solid sphere and to model its characteristics

O trabalho apresenta uma investigação sobre a influência da umidade atmosférica no processo de absorção de oxigênio atmosférico por corpo de água através de sua superfície líquida livre. Os experimentos realizados em laboratório consistem na reoxigenação de uma massa de água, contida em um tanque cilíndrico, submetida à agitação mecânica. A atmosfera que reabastece de oxigênio a massa líquida é controlada e os ensaios são conduzidos com vários níveis de umidade do ar, o que provoca diferentes taxas de evaporação. Simultaneamente, determinam-se os coeficientes de reoxigenação, K2 (h-1), em cada experimento. Investiga-se neste trabalho a correlação entre esses dois parâmetros. O processo de reoxigenação é analisado inicialmente com o uso de metodologia clássica baseada em modelos matemáticos tradicionais (possivelmente inadequados). Propõe-se neste trabalho, um modelo original para essa mesma análise. / The influence of the atmospheric humidity on the process of absorption of oxygen by a water body through its free surface is presented herein. Laboratory experiments were run for the reoxygenation of a water mass kept in a cylindrical vessel under mechanical agitation. The quality of the atmospheric air transferring oxygen to water is controlled and the tests are run with several levels of air humidity, what renders different rates of evaporation. The corresponding coefficients of reaeration K2 (h-1) are determined for each experiment. The correlation between these two latter parameters is investigated. The process of reoxygenation is analyzed initially using a classical methodology based on traditional mathematical models (possibly inadequate). An original model for the same analysis is proposed in this work.

Uma das dificuldades relacionadas com a exploração de petróleo é o transporte de óleo pesado, que devido a sua alta viscosidade, acarreta em uma elevada perda de carga no sistema. Para proporcionar economia de energia aplica-se o método do Core Annular Flow (CAF) onde é utilizado um escoamento anular bifásico em que a água escoa na periferia da tubulação para redução do gasto energético. O presente trabalho visou compreender e reproduzir este fenômeno, desenvolvendo simulações em CFD através do pacote comercial ANSYS FLUENT considerando o escoamento 3D, turbulento, isotérmico e incompressível para casos estacionários e transientes. A interface entre a água e o óleo foi adequadamente reproduzida em diferentes geometrias como tubo reto e com curva. O método LES para simulação de grandes escalas provou ser o melhor método de turbulência dentre os testados, como k-epsilon e modelo de tensores de Reynolds, de forma com que a interface fosse representada corretamente. O modelo para sistema multifásico adotado foi o Volume de Fluido (VOF), comparado com o comportamento experimental e com dados da literatura. Os fenômenos de swirl observados experimentalmente também foram reproduzidos de forma satisfatória. / One of the difficulties related to oil exploration is the transportation of heavy oil, which due to its high viscosity, causes a high pressure drop in the system. In order to provide energy savings, the Core Annular Flow (CAF) method applies where a two-phase annular flow occurs in which water flows at the periphery adjacent to the pipe to reduce energy expenditure. The present work aimed to understand and reproduce this phenomenon, developing CFD simulations through the commercial package ANSYS FLUENT considering flow as 3D, turbulent, isothermal and incompressible for stationary and transient cases. The interface between water and oil has been properly reproduced in different geometries such as straight pipe and pipe with a curve. The LES method for large scale simulation proved to be the best turbulence method among the tested, such as k-epsilon and Reynolds stress model, so that the interface was correctly represented. The model for the multiphase system adopted was the Volume of Fluid (VOF), compared to the experimental behavior and with data from the literature. The experimentally observed swirl phenomena were also reproduced satisfactorily.

Uma das dificuldades relacionadas com a exploração de petróleo é o transporte de óleo pesado, que devido a sua alta viscosidade, acarreta em uma elevada perda de carga no sistema. Para proporcionar economia de energia aplica-se o método do Core Annular Flow (CAF) onde é utilizado um escoamento anular bifásico em que a água escoa na periferia da tubulação para redução do gasto energético. O presente trabalho visou compreender e reproduzir este fenômeno, desenvolvendo simulações em CFD através do pacote comercial ANSYS FLUENT considerando o escoamento 3D, turbulento, isotérmico e incompressível para casos estacionários e transientes. A interface entre a água e o óleo foi adequadamente reproduzida em diferentes geometrias como tubo reto e com curva. O método LES para simulação de grandes escalas provou ser o melhor método de turbulência dentre os testados, como k-epsilon e modelo de tensores de Reynolds, de forma com que a interface fosse representada corretamente. O modelo para sistema multifásico adotado foi o Volume de Fluido (VOF), comparado com o comportamento experimental e com dados da literatura. Os fenômenos de swirl observados experimentalmente também foram reproduzidos de forma satisfatória. / One of the difficulties related to oil exploration is the transportation of heavy oil, which due to its high viscosity, causes a high pressure drop in the system. In order to provide energy savings, the Core Annular Flow (CAF) method applies where a two-phase annular flow occurs in which water flows at the periphery adjacent to the pipe to reduce energy expenditure. The present work aimed to understand and reproduce this phenomenon, developing CFD simulations through the commercial package ANSYS FLUENT considering flow as 3D, turbulent, isothermal and incompressible for stationary and transient cases. The interface between water and oil has been properly reproduced in different geometries such as straight pipe and pipe with a curve. The LES method for large scale simulation proved to be the best turbulence method among the tested, such as k-epsilon and Reynolds stress model, so that the interface was correctly represented. The model for the multiphase system adopted was the Volume of Fluid (VOF), compared to the experimental behavior and with data from the literature. The experimentally observed swirl phenomena were also reproduced satisfactorily.

Les systèmes d’actionnement à distance pour la manipulation d’objets de taille micrométrique ont connu un développement sans précédent ces dernières années dans les laboratoires de recherche. Ils permettent de contrôler à distance le déplacement et l’orientation d’objets en appliquant des champs de force à distance. Ils sont donc spécialement adaptés pour agir dans des milieux confinés pour lesquels les problèmes d’accessibilité empêchent l’utilisation de manipulateurs robotisés classiques. De plus la faible inertie de ces systèmes permet d’atteindre des cadences de manipulation importantes. Parmi les effets physiques exploitables pour actionner ces systèmes une attention particulière est portée sur les effets magnétiques, en raison des niveaux de forces élevés atteignables. L’état de l’art montre un nombre de travaux importants dans le domaine de l’actionnement magnétique en environnement liquide. Cependant les vitesses atteignables sont limitées par les frottements visqueux. Quelques études font état de l’utilisation de l’actionnement magnétique en milieu ambiant, mais les forces d’adhésion entre le substrat et la particule rend le système peu répétable. Cette thèse propose une approche originale alliant faibles frottements visqueux et grande répétabilité en considérant un milieu de travail peu étudié : l’interface air/liquide. Cette thèse s’intéresse plus particulièrement à la modélisation, la caractérisation, l’analyse des performances et la commande d’un système d’actionnement magnétique à l’interface air/liquide pour des applications à l’échelle micrométrique. / In recent years research laboratories have shown an increasing interest for non-contact actuation systems at micrometer scale. These systems control both the displacement and the orientation of the objects using remote force fields. They are of major interest in confined spaces in which traditional approaches based on robotic grippers are not suitable. In addition high manipulation throughputs can be reached due to the low inertia of these systems. Several physical principles can be considered as the actuation source. Among them a special attention is given to magnetic forces due to the high forces that can be applied to the objects. A large amount of work has been carried out on magnetic actuation systems for manipulation in liquid environments. However velocities are limited by viscous effects. A few studies are reported on magnetic systems in ambient environments. However repeatability is decreased by adhesion forces between the substrate and the objects. This work proposes an original approach with a good trade off between low viscous effects and high repeatability based on the use of a specific environment: the air/liquid interface. This thesis presents the modelling, the characterization, the performance analysis and the control of a magnetic actuation system at the air/liquid interface for applications at the micrometer scale.