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THERMODYNAMICS FUNDAMENTALS AND ITS APPLICATION IN SCIENCE Edited by Ricardo Morales-Rodriguez THERMODYNAMICS – FUNDAMENTALS AND ITS APPLICATION IN SCIENCE Edited by Ricardo Morales-Rodriguez Thermodynamics – Fundamentals and Its Application in Science http://dx.doi.org/10.5772/2615 Edited by Ricardo Morales-Rodriguez Contributors Ahmet Gürses, Mehtap Ejder-Korucu, Nikolai Bazhin, Yi Fang, Bohdan Hejna, A. Plastino, Evaldo M. F. Curado, M. Casas, Zdeňka Kolská, Milan Zábranský, Alena Randová, Ronald J. Bakker, Elisabeth Blanquet, Ioana Nuta, Lin Li, Rıza Atav, L.E. Panin, Yu Liu, Kui Wang, Philippe Vieillard, Nong-Moon Hwang, Jae-Soo Jung, Dong-Kwon Lee, Vasiliy Fefelov, Vitaly Gorbunov, Alexander Myshlyavtsev, Marta Myshlyavtseva, Adela Ionescu, Paiguy Armand Ngouateu Wouagfack, Réné Tchinda, Raul Măluţan, Pedro Gómez Vilda, Xuejing Hou, Harvey J.M. Hou, C.A.S. Silva, Hui-Zhen Fu, Yuh-Shan Ho Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Marina Jozipovic Typesetting InTech Prepress, Novi Sad Cover InTech Design Team First published September, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Thermodynamics – Fundamentals and Its Application in Science, Edited by Ricardo Morales-Rodriguez p. cm. ISBN 978-953-51-0779-8 Contents Preface IX Section 1 Classical Thermodynamics 1 Chapter 1 A View from the Conservation of Energy to Chemical Thermodynamic 3 Ahmet Gürses and Mehtap Ejder-Korucu Chapter 2 Useful Work and Gibbs Energy 29 Nikolai Bazhin Section 2 Statistical Thermodynamics 45 Chapter 3 Gibbs Free Energy Formula for Protein Folding 47 Yi Fang Chapter 4 Information Capacity of Quantum Transfer Channels and Thermodynamic Analogies 83 Bohdan Hejna Chapter 5 Thermodynamics’ Microscopic Connotations 119 A. Plastino, Evaldo M. F. Curado and M. Casas Section 3 Property Prediction and Thermodynamics 133 Chapter 6 Group Contribution Methods for Estimation of Selected Physico-Chemical Properties of Organic Compounds 135 Zdeňka Kolská, Milan Zábranský and Alena Randová Chapter 7 Thermodynamic Properties and Applications of Modified van-der-Waals Equations of State 163 Ronald J. Bakker Chapter 8 Thermodynamics Simulations Applied to Gas-Solid Materials Fabrication Processes 191 Elisabeth Blanquet and Ioana Nuta VI Contents Section 4 Material and Products 215 Chapter 9 Application of Thermodynamics and Kinetics in Materials Engineering 217 Lin Li Chapter 10 Thermodynamics of Wool Dyeing 247 Rıza Atav Chapter 11 Mesomechanics and Thermodynamics of Nanostructural Transitions in Biological Membranes Under the Action of Steroid Hormones 263 L.E. Panin Chapter 12 Thermodynamics of Resulting Complexes Between Cyclodextrins and Bile Salts 305 Yu Liu and Kui Wang Chapter 13 Thermodynamics of Hydration in Minerals: How to Predict These Entities 339 Philippe Vieillard Chapter 14 Thermodynamics and Kinetics in the Synthesis of Monodisperse Nanoparticles 371 Nong-Moon Hwang, Jae-Soo Jung and Dong-Kwon Lee Chapter 15 Statistical Thermodynamics of Lattice Gas Models of Multisite Adsorption 389 Vasiliy Fefelov, Vitaly Gorbunov, Alexander Myshlyavtsev and Marta Myshlyavtseva Section 5 Non-Equilibrium Thermodynamics 417 Chapter 16 Influence of Simulation Parameters on the Excitable Media Behaviour – The Case of Turbulent Mixing 419 Adela Ionescu Chapter 17 ECOP Criterion for Irreversible Three-Heat-Source Absorption Refrigerators 445 Paiguy Armand Ngouateu Wouagfack and Réné Tchinda Section 6 Thermodynamics in Diverse Areas 461 Chapter 18 Thermodynamics of Microarray Hybridization 463 Raul Măluţan and Pedro Gómez Vilda Chapter 19 Probing the Thermodynamics of Photosystem I by Spectroscopic and Mutagenic Methods 483 Xuejing Hou and Harvey J.M. Hou Contents VII Chapter 20 Fuzzy Spheres Decays and Black Hole Thermodynamics 501 C.A.S. Silva Chapter 21 Bibliometric Analysis of Thermodynamic Research: A Science Citation Index Expanded-Based Analysis 519 Hui-Zhen Fu and Yuh-Shan Ho Preface This book is a result of a careful selection of scientific contributions involved in the thermodynamic area and it is titled “Thermodynamics - Fundamentals and Its Application in Science”. Thermodynamics is very important for the description of phenomena in different fields on science. Therefore, this book contains chapters describing the fundamentals and the diverse applications in different areas under development, which allow the access of different kind of readers; for instance, bachelor and postgraduate students, researchers, etc. The book is divided in six sections and the classification was done according to the purpose, relevance and approaches employed in the development of the contributions. The first section describes the classical thermodynamics, where firstly an overview about classical thermodynamics considering diverse fundamental concepts of the area is described. This section also has a contribution presenting the mechanism of useful work and heat production in reversible systems. The second section includes some chapters based on statistical mechanics, for instance, one of the chapters described the protein folding phenomena based on Gibbs free energy through the use of quantum mechanics, topic of high importance currently. On the other hand, another of the contributions in this section describes the information capacity of quantum transfer channels and thermodynamics analogies. The last chapter of this section introduces some axioms which allow one to derive the MaxEnt equations and viceversa, giving an alternative foundation for equilibriums statistical mechanics. The property prediction in thermodynamics is presented in the following section. A chapter explaining the use and implementation of group contribution methods for property prediction of organic compounds is firstly described. The description of pure gases and multi/component fluid systems is presented in another chapter, which in fact used a modified version of the Van der Waals equation. The last chapter is this section illustrates the interest area of macroscopic modelling on the thermodynamics simulation and gives some interesting examples in different domains in the material and product design areas employing some predicted properties. The fourth section contains the application of some thermodynamic insights in the material and products area. One of the chapters introduces some computational X Preface results on the designing of advances material. A wool dyeing phenomenon described by thermodynamics is presented in another contribution. On the other hand, some authors talk about nanostructural transition in biological membranes under the action of steroid hormones. In this section, a chapter highlighting the importance of improving the understanding of molecular recognition mechanics in supramolecular systems and the design and synthesis of new supramolecular systems based on different kinds of cyclodextrins is also presented. The use of thermodynamics in the mineral field is presented describing the hydration of minerals providing several relationships illustrated by examples exhibiting great variability closely related to the chemical and physical compound properties. The synthesis of monodisperse nanoparticles is also described in one of the chapters of this section, relying on thermodynamics and kinetic basis. The last chapter of the section talks about thermodynamics of lattice gas models of multisite adsorption. A section with chapters presenting non equilibrium approach is the fifth section of the book. One of the chapters talks about the influence of certain parameters on excitable media behaviour, specifically describing the turbulent mixing. Moreover, the other chapter of this section presents an analytical method developed to achieve the performance optimization of irreversible three-heat-sources absorption refrigeration models having finite-rate of heat transfer, heat leakage and internal irreversibility based on an objective function named ecological coefficient performance (ECOP). The last section contains some chapters talking about diverse applications of thermodynamics. For instance, one chapter discusses the importance of thermodynamics in microarrays hybridization, due to thermodynamics factors affect molecular interaction which in fact are not taken into account for the estimation of genetic expression in current algorithms. Another chapter describes a case study probing thermodynamics of electron transfer in photosystems using a combination of molecular genetics and sophisticated biophysical techniques, in particular, pulsed photoacoustic spectroscopy. The other chapter of this section address the black hole thermodynamics in the context of topology change, as conceived for some classes of quantum spaces called fuzzy spheres. The last chapter of the section and book shows a bibliometric study about thermodynamic contributions giving a general picture about the number of papers, institutions and countries working on certain thermodynamic topics as well as the quality of the paper by their citations. It is expected that the collections of these chapters contributes to the state of the art in the thermodynamics area, which not only involve the fundamentals of thermodynamics, but moreover, consider the wide applications of this area in several fields. Ricardo Morales-Rodriguez Technical University of Denmark, Denmark