This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.
This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.
A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.
The contributed volume puts emphasis on a superior role of water in (bio)systems exposed to a mechanical stimulus. It is well known that water plays an extraordinary role in our life. It feeds mammalian or other organism after distributing over its whole volume to support certain physiological and locomotive (friction-adhesion) processes to mention but two of them, both of extreme relevance. Water content, not only in the mammalian organism but also in other biosystems such as whether those of soil which is equipped with microbiome or the ones pertinent to plants, having their own natural network of water vessels, is always subjected to a force field.The decisive force field applied to the biosystems makes them biomechanically agitated irrespective of whether they are subjected to external or internal force-field conditions. It ought to be noted that the decisive mechanical factor shows up in a close relation with the space-and-time scale in which it is causing certain specific phenomena to occur.The scale problem, emphasizing the range of action of gravitational force, thus the millimeter or bigger force vs. distance scale, is supposed to enter the so-called macroscale approach to water transportation through soil or plants’ roots system. It is merely related to a percolation problem, which assumes to properly inspect the random network architecture assigned to the biosystems invoked. The capillarity conditions turn out to be of prior importance, and the porous-medium effect has to be treated, and solved in a fairly approximate way.The deeper the scale is penetrated by a force-exerting and hydrated agent the more non-gravitational force fields manifest. This can be envisaged in terms of the corresponding thermodynamic (non-Newtonian) forces, and the phenomena of interest are mostly attributed to suitable changes of the osmotic pressure. In low Reynolds number conditions, thus in the (sub)micrometer distance-scale zone, they are related with the corresponding viscosity changes of the aqueous, e.g. cytoplasmatic solutions, of semi-diluted and concentrated (but also electrolytic) characteristics. For example, they can be observed in articulating systems of mammals, in their skin, and to some extent, in other living beings, such as lizards, geckos or even insects. Through their articulating devices an external mechanical stimulus is transmitted from macro- to nanoscale, wherein the corresponding osmotic-pressure conditions apply. The content of the proposed work can be distributed twofold. First, the biomechanical mammalian-type (or, similar) systems with extraordinary relevance of water for their functioning will be presented, also including a presentation of water itself as a key physicochemical system/medium. Second, the suitably chosen related systems, mainly of soil and plant addressing provenience, will be examined thoroughly. As a common denominator of all of them, it is proposed to look at their hydrophobic and/or (de)hydration effects, and how do they impact on their basic mechanical (and related, such as chemo-mechanical or piezoelectric, etc.) properties. An additional tacit assumption employed throughout the monograph concerns statistical scalability of the presented biosystems which is equivalent to take for granted a certain similarity between local and global system’s properties, mostly those of mechanical nature. The presented work’s chapters also focus on biodiversity and ecological aspects in the world of animals and plants, and the related systems. The chapters’ contents underscore the bioinspiration as the key landmark of the proposed monograph.
The contributed volume puts emphasis on a superior role of water in (bio)systems exposed to a mechanical stimulus. It is well known that water plays an extraordinary role in our life. It feeds mammalian or other organism after distributing over its whole volume to support certain physiological and locomotive (friction-adhesion) processes to mention but two of them, both of extreme relevance. Water content, not only in the mammalian organism but also in other biosystems such as whether those of soil which is equipped with microbiome or the ones pertinent to plants, having their own natural network of water vessels, is always subjected to a force field.The decisive force field applied to the biosystems makes them biomechanically agitated irrespective of whether they are subjected to external or internal force-field conditions. It ought to be noted that the decisive mechanical factor shows up in a close relation with the space-and-time scale in which it is causing certain specific phenomena to occur.The scale problem, emphasizing the range of action of gravitational force, thus the millimeter or bigger force vs. distance scale, is supposed to enter the so-called macroscale approach to water transportation through soil or plants’ roots system. It is merely related to a percolation problem, which assumes to properly inspect the random network architecture assigned to the biosystems invoked. The capillarity conditions turn out to be of prior importance, and the porous-medium effect has to be treated, and solved in a fairly approximate way.The deeper the scale is penetrated by a force-exerting and hydrated agent the more non-gravitational force fields manifest. This can be envisaged in terms of the corresponding thermodynamic (non-Newtonian) forces, and the phenomena of interest are mostly attributed to suitable changes of the osmotic pressure. In low Reynolds number conditions, thus in the (sub)micrometer distance-scale zone, they are related with the corresponding viscosity changes of the aqueous, e.g. cytoplasmatic solutions, of semi-diluted and concentrated (but also electrolytic) characteristics. For example, they can be observed in articulating systems of mammals, in their skin, and to some extent, in other living beings, such as lizards, geckos or even insects. Through their articulating devices an external mechanical stimulus is transmitted from macro- to nanoscale, wherein the corresponding osmotic-pressure conditions apply. The content of the proposed work can be distributed twofold. First, the biomechanical mammalian-type (or, similar) systems with extraordinary relevance of water for their functioning will be presented, also including a presentation of water itself as a key physicochemical system/medium. Second, the suitably chosen related systems, mainly of soil and plant addressing provenience, will be examined thoroughly. As a common denominator of all of them, it is proposed to look at their hydrophobic and/or (de)hydration effects, and how do they impact on their basic mechanical (and related, such as chemo-mechanical or piezoelectric, etc.) properties. An additional tacit assumption employed throughout the monograph concerns statistical scalability of the presented biosystems which is equivalent to take for granted a certain similarity between local and global system’s properties, mostly those of mechanical nature. The presented work’s chapters also focus on biodiversity and ecological aspects in the world of animals and plants, and the related systems. The chapters’ contents underscore the bioinspiration as the key landmark of the proposed monograph.
This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
Fundamentals of Molecular Structural Biology reviews the mathematical and physical foundations of molecular structural biology. Based on these fundamental concepts, it then describes molecular structure and explains basic genetic mechanisms. Given the increasingly interdisciplinary nature of research, early career researchers and those shifting into an adjacent field often require a "fundamentals" book to get them up-to-speed on the foundations of a particular field. This book fills that niche.
This book was planned and written with one central goal in mind: to demonstrate that statistical thermodynamics can be used successfully by a broad group of scientists, ranging from chemists through biochemists to biologists, who are not and do not intend to become specialists in statistical thermodynamics. The book is addressed mainly to gradu ate students and research scientists interested in designing experiments the results of which may be interpreted at the molecular level, or in interpreting such experimental results. It is not addressed to those who intend to practice statistical thermodynamics per se. With this goal in mind, I have expended a great deal of effort to make the book clear, readable, and, I hope, enjoyable. This does not necessarily mean that the book as a whole is easy to read. The first four chapters are very detailed. The last four become progressively more difficult to read, for several reasons. First, presuming that the reader has already acquired familiarity with the methods and arguments presented in the first part, I felt that similar arguments could be skipped later on, leaving the details to be filled in by the reader. Second, the systems themselves become progressively more com plicated as we proceed toward the last chapter.
The First Conference on materials science and engineering, including physics, physical chemistry, condensed matter chemistry, and technology in general, was held in September 1995, in Herceg Novi. An initiative to establish Yugoslav Materials Research Society was born at the conference and, similar to other MR societies in the world, the programme was made and objectives determined. The Yugoslav Materials Research Society (Yu-MRS), a nongovernment and non-profit scientific association, was founded in 1997 to promote multidisciplinary goal-oriented research in materials science and engineering. The main task and objective of the Society has been to encourage creativity in materials research and engineering to reach a harmonic coordination between achievements in this field in our country and analogous activities in the world with an aim to include our country into global international projects. Until 2003, Conferences were held every second year and then they grew into Annual Conferences that were traditionally held in Herceg Novi in September of every year. In 2007 Yu-MRS formed two new MRS: MRS-Serbia (official successor of Yu-MRS) and MRS-Montenegro (in founding). In 2008, MRS – Serbia became a member of FEMS (Federation of European Materials Societies). The Twelfth Annual Conference YUCOMAT 2010 was held on September 6-10, 2010 in Heceg Novi, Montenegro
