Morphed Potential Energy Surfaces From The Spectroscopy Of Weakly Bound Complexes

Author by : Luis A. Rivera-Rivera
Languange : en
Publisher by : Unknown
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Description : In this research the so-called potential morphing method was used to generate reliable interaction potential energy surfaces for weakly bound complexes. The potential morphing method is based on the optimization of modified computed ab initio potential energy surfaces to give predicted spectroscopic data, in agreement with the experimental values. In the standard potential morphing procedure the computed ab initio potential is adjusted by scaling, shifting, and dilating transformations to reproduce the experimental data. In this research, selected systems have been chosen to be studied based on the availability of varied and accurate sets of experimental data. In the present work, accurate interaction potential energy surfaces are obtained for the weakly bound complexes: Ne:HCl, OC:HX (X = F, Cl, Br, I) and HI:CO2. A comprehensive study on the interaction potential of these systems provides fundamental perspectives on the influence of different intermolecular forces. In addition the ground state isotopic isomerization observed in the OC:HI system may suggest a possible structural change of proteins, and other biological macromolecules, in deuterated solvents. In this dissertation, an alternative approach to morphing the potential energy surfaces of non-covalent interactions is also presented. In this approach the morphed potential is generated as a linear combination of ab initio potentials, that are computed at different levels of theory. This new morphing approach is applied to OC:HCl and is found to be of similar accuracy to that of the previous morphing method. In addition, this new method is also extended from four-dimensions to six-dimensions and is applied to the OC:HF system to obtain a vibrationally-complete six-dimensional morphed potential.


Spectroscopy Of Biological Molecules New Directions

Author by : Jan Greve
Languange : en
Publisher by : Springer Science & Business Media
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Description : Investigation of the structure and function of biological molecules through spectroscopic methods is a field rich in revealing, clever techniques and demanding experiments. It is most gratifying to see that the basic concepts are applied to more and more complex systems, making feasible the study of the behaviour of whole systems in relation to molecular disturbances. The analytical potential of spectroscopy and spectroscopic imaging enables species identification of bacteria and tissue recognition. Clear opportunities for in vivo applications become apparent in the medical field. The methods developed in biophysics start to generate spin-off in the direction of biotechnology, where in previous years we have seen this happen for biochemical techniques. New directions are manifest. Tools are being developed to investigate the behaviour of single molecules in interaction with their environment. Individual interactions can now be investigated and individual molecules in complexes can be visualized. Processes that were previously unobservable as a result of ensemble averaging can now be investigated on a single molecule level. Completely new information with regard to molecular behaviour is obtained in this way. The insights amaze us and the prospect that this development will continue is exciting. The 8th European Conference on the Spectroscopy of Biological Molecules is proud to have contributed to the dissemination of these new directions. This proceedings book is an appropriate reflection of the progress obtained so far in the spectroscopy of biological molecules.


Quantum Chemistry Simulation Of Biological Molecules

Author by : Eudenilson L. Albuquerque
Languange : en
Publisher by : Cambridge University Press
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Description : Nano-biotechnology crosses the boundaries between physics, biochemistry and bioengineering, and has profound implications for the biomedical engineering industry. This book describes the quantum chemical simulation of a wide variety of molecular systems, with detailed analysis of their quantum chemical properties, individual molecular configurations, and cutting-edge biomedical applications. Topics covered include the basic properties of quantum chemistry and its conceptual foundations, the nanoelectronics and thermodynamics of DNA, the optoelectronic properties of the five DNA/RNA nucleobase anhydrous crystals, and key examples of molecular diode prototypes. A wide range of important applications are described, including protein binding of drugs such as cholesterol-lowering, anti-Parkinson and anti-migraine drugs, and recent developments in cancer biology are also discussed. This modern and comprehensive text is essential reading for graduate students and researchers in multidisciplinary areas of biological physics, chemical physics, chemical engineering, biochemistry and bioengineering.


Water And Biological Macromolecules

Author by : Anonim
Languange : en
Publisher by : Macmillan International Higher Education
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Physics And Chemistry At Low Temperatures

Author by : Leonid Khriachtchev
Languange : en
Publisher by : CRC Press
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Description : Tunneling reactions in chemistry are characterized by the low-temperature limit when the classical contribution is negligible. Many practical applications benefit from the lack of heat and have a deep physical basis. Interesting advantages of chemical synthesis at low temperatures have also been demonstrated. This book covers fundamental and practical aspects of the processes and experimental and theoretical methods used in the field. The chapters are written by leading scientists who have very strong experience in the selected topics, and many practical recommendations can be found in this book.


Bioinformatics

Author by : Horacio Pérez-Sánchez
Languange : en
Publisher by : BoD – Books on Demand
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Description : This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here.


Reviews In Computational Chemistry

Author by : Kenny B. Lipkowitz
Languange : en
Publisher by : John Wiley & Sons
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Description : This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts. In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics. Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.


Spectroscopy Of Biological Molecules

Author by : Camille Sandorfy
Languange : en
Publisher by : Springer Science & Business Media
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Description : This volume contains the proceedings of the NATO-Advanced Study Institute on the "Spectroscopy of Biological Molecules", which took place on July 4-15, 1983 in Acquafredda di Maratea, Italy. The institute concentrated on three main subiects: the structure and dymanics of DNA, proteins, and visual and plant pigments. Its timeliness has been linked to rapid advances in certain spectroscopic techniques which yielded a consider able amount of new information on the structure and inter actions of biologically important molecules. Among these techniques Fourier transform infrared, resonance and surface enhanced 'Raman spectroscopies, Raman microscopy and micro probing, time resolved techniques, two photon and ultrafast electronic, and C-13, N-15 and P-31 NMR spectroscopies and kinetic and static IR difference spectroscopy receiced a great deal of attention at the Institute. In addition, an entirely new technique, near-millimeter-wave spectroscopy has been presented and discussed. Two introductory quantum chemical lectures, one on the structure of water in DNA, and another pn the energy bands in DNA and proteins set the stage for the experimentally oriented lectures that followed. Fundamental knowledge on hydrogen bonding was the topic of two other lectures. Panel discussions were held on the structure and confor mations of DNA, metal-DNA adducts and proteins and on visual pigments. Many scientists who normally attend different conferences and never meet, met at Aquafredda di Maratea. We feel, that at the end of our Institute a synthetic vi~w emerged on the powerful spectroscopic and theoretical methods which are now available for the study of biological molecules.


Strength From Weakness Structural Consequences Of Weak Interactions In Molecules Supermolecules And Crystals

Author by : Aldo Domenicano
Languange : en
Publisher by : Springer Science & Business Media
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Description : The accurate determination of the structure of molecular systems provides information about the consequences of weak interactions both within and between molecules. These consequences impact the properties of the materials and the behaviour in interactions with other substances. The book presents modern experimental and computational techniques for the determination of molecular structure. It also highlights applications ranging from the simplest molecules to DNA and industrially significant materials. Readership: Graduate students and researchers in structural chemistry, computational chemistry, molecular spectroscopy, crystallography, supramolecular chemistry, solid state chemistry and physics, and materials science.


Dynamics And The Problem Of Recognition In Biological Macromolecules

Author by : Oleg Jardetzky
Languange : en
Publisher by : Springer Science & Business Media
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Description : From within complex structures of organisms and cells down to the molecular level, biological processes all involve movement. Muscular fibers slide on each other to activate the muscle, as polymerases do along nucleic acids for replicating and transcribing the genetic material. Cells move and organize themselves into organs by recognizing each other through macromolecular surface-specific interactions. These recognition processes involve the mu tual adaptation of structures that rely on their flexibility. All sorts of conformational changes occur in proteins involved in through-membrane signal transmission, showing another aspect of the flexibility of these macromolecules. The movement and flexibility are inscribed in the polymeric nature of essential biological macromolecules such as proteins and nucleic acids. For instance, the well-defined structures formed by the long protein chain are held together by weak noncovalent interac tions that design a complex potential well in which the protein floats, permanently fluctuating between several micro- or macroconformations in a wide range of frequencies and ampli tudes. The inherent mobility of biomolecular edifices may be crucial to the adaptation of their structures to particular functions. Progress in methods for investigating macromolecular structures and dynamics make this hypothesis not only attractive but more and more testable.


Spectroscopy Of Biological Molecules

Author by : M.P. Marques
Languange : en
Publisher by : IOS Press
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Description : This book presents contributions from some of the leading experts in spectroscopic techniques including infrared, Raman, NMR, fluorescence and Circular Dichroism spectroscopy. Structural characterization of biomolecules, cells, tissues and whole organisms are amongst the topics that were covered by these experts at the 14th European Conference on Spectroscopy of Biological Molecules (ECSBM2011), held at the University of Coimbra, Portugal, from 29th August to 3rd September 2011, of which this book contains the papers. The book would be particularly valuable for those interested in vibrational spectroscopy and imaging of cells and tissues, applications of spectroscopy in biotechnology, single cell studies and microbial characterization. It highlights the potential of spectroscopy and imaging in medical diagnosis and screening, and discusses issues related to methodology, including data acquisition, analysis and processing, that would be valuable for scientists who are new to the field. The book would be an important reference source for scientists in academia and industry as well as early stage researchers such as graduate students and post-doctoral researchers.


Molecules In Physics Chemistry And Biology

Author by : J. Maruani
Languange : en
Publisher by : Springer Science & Business Media
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Description : Volume 1: General Introduction to Molecular Sciences Volume 2: Physical Aspects of Molecular Systems Volume 3: Electronic Structure and Chemical Reactivity Volume 4: Molecular Phenomena in Biological Sciences


Gas Phase Ir Spectroscopy And Structure Of Biological Molecules

Author by : Anouk M. Rijs
Languange : en
Publisher by : Springer
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Description : The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students.


Molecules In Physics Chemistry And Biology

Author by : Jean Maruani
Languange : en
Publisher by : Springer Science & Business Media
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Total Read : 38
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Description : Volume 1: General Introduction to Molecular Sciences Volume 2: Physical Aspects of Molecular Systems Volume 3: Electronic Structure and Chemical Reactivity Volume 4: Molecular Phenomena in Biological Sciences


Spectroscopy Of Biological Molecules

Author by : Jean Claude Merlin
Languange : en
Publisher by : Springer
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Description : 6th European Conference on the Spectroscopy of Biological Molecules, 3--8 September 1995, Villeneuve d'Ascq, France


Principles Of Nanotechnology

Author by : G. Ali Mansoori
Languange : en
Publisher by : World Scientific
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Description : - Gives unified presentation of many of the major principles in nanotechnology: molecular-based study of condensed matter in small systems. - Authored by an expert in the molecular-based study of matter - Accessible to students, yet of interest to experts - Emphasizes the intrinsic beauty of methods of bottom-up nanotechnology - Includes many full-color figures


Intermolecular Potential Functions From Spectroscopic Properties Of Weakly Bound Complexes

Author by : Anonim
Languange : en
Publisher by : Unknown
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Description : Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH)2, (CO2)2, HCCH - CO2; it had to be modified to work with HX dimers and CO2-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH)3, CO2 containing complexes, (HX)2, HX - CO2, CO2 - CO, (CO2)3, and (OCS)2. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC).


Molecular Dynamics

Author by : Lichang Wang
Languange : en
Publisher by : BoD – Books on Demand
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Description : Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines


Essentials Of Chemical Biology

Author by : Andrew D. Miller
Languange : en
Publisher by : John Wiley & Sons
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Description : “This excellent work fills the need for an upper-level graduate course resource that examines the latest biochemical, biophysical, and molecular biological methods for analyzing the structures and physical properties of biomolecules... This reviewer showed [the book] to several of his senior graduate students, and they unanimously gave the book rave reviews. Summing Up: Highly recommended...” CHOICE Chemical biology is a rapidly developing branch of chemistry, which sets out to understand the way biology works at the molecular level. Fundamental to chemical biology is a detailed understanding of the syntheses, structures and behaviours of biological macromolecules and macromolecular lipid assemblies that together represent the primary constituents of all cells and all organisms. The subject area of chemical biology bridges many different disciplines and is fast becoming an integral part of academic and commercial research. This textbook is designed specifically as a key teaching resource for chemical biology that is intended to build on foundations lain down by introductory physical and organic chemistry courses. This book is an invaluable text for advanced undergraduates taking biological, bioorganic, organic and structural chemistry courses. It is also of interest to biochemists and molecular biologists, as well as professionals within the medical and pharmaceutical industry. Key Features: A comprehensive introduction to this dynamic area of chemistry, which will equip chemists for the task of understanding and studying the underlying principles behind the functioning of biological macro molecules, macromolecular lipid assemblies and cells. Covers many basic concepts and ideas associated with the study of the interface between chemistry and biology. Includes pedagogical features such as: key examples, glossary of equations, further reading and links to websites. Clearly written and richly illustrated in full colour.


Informational Biopolymers Of Genes And Gene Expression

Author by : R.D. Blake
Languange : en
Publisher by : University Science Books
Format Available : PDF, ePub, Mobi
Total Read : 80
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Description : This new text examines thebiophysics and biochemistry of nucleic acids and proteins, carving outthe dynamic interface between chemistry and molecular biology, and providing adetailed picture of nucleic acids and proteins, their structures, biologicalproperties, and origins and evolution.


Introduction To Biophysical Methods For Protein And Nucleic Acid Research

Author by : Jay A. Glasel
Languange : en
Publisher by : Academic Press
Format Available : PDF, ePub, Mobi
Total Read : 84
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Description : The first of its kind, Introduction to Biophysical Methods for Protein and Nucleic Acid Research serves as a text for the experienced researcher and student requiring an introduction to the field. Each chapter presents a description of the physical basis of the method, the type of information that may be obtained with the method, how data should be analyzed and interpreted and, where appropriate, practical tips about procedures and equipment. Key Features * Modern Use of Mass Spectroscopy * NMR Spectroscopy * Molecular Modeling and Graphics * Macintosh and DOS/Windows 3.x disks


Equilibria And Kinetics Of Biological Macromolecules

Author by : Prof. Jan Hermans
Languange : en
Publisher by : John Wiley & Sons
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Description : Progressively builds a deep understanding of macromolecular behavior Based on each of the authors' roughly forty years of biophysics research and teaching experience, this text instills readers with a deep understanding of the biophysics of macromolecules. It sets a solid foundation in the basics by beginning with core physical concepts such as thermodynamics, quantum chemical models, molecular structure and interactions, and water and the hydrophobic effect. Next, the book examines statistical mechanics, protein-ligand binding, and conformational stability. Finally, the authors address kinetics and equilibria, exploring underlying theory, protein folding, and stochastic models. With its strong emphasis on molecular interactions, Equilibria and Kinetics of Biological Macromolecules offers new insights and perspectives on proteins and other macromolecules. The text features coverage of: Basic theory, applications, and new research findings Related topics in thermodynamics, quantum mechanics, statistical mechanics, and molecular simulations Principles and applications of molecular simulations in a dedicated chapter and interspersed throughout the text Macromolecular binding equilibria from the perspective of statistical mechanics Stochastic processes related to macromolecules Suggested readings at the end of each chapter include original research papers, reviews and monographs, enabling readers to explore individual topics in greater depth. At the end of the text, ten appendices offer refreshers on mathematical treatments, including probability, computational methods, Poisson equations, and defining molecular boundaries. With its classroom-tested pedagogical approach, Equilibria and Kinetics of Biological Macromolecules is recommended as a graduate-level textbook for biophysics courses and as a reference for researchers who want to strengthen their understanding of macromolecular behavior.


New Algorithms For Macromolecular Simulation

Author by : Benedict Leimkuhler
Languange : en
Publisher by : Springer Science & Business Media
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Total Read : 38
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Description : Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.


Biomacromolecules

Author by : C. Stan Tsai
Languange : en
Publisher by : Wiley-Liss
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Total Read : 60
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Description : Provides an integrated presentation of the structure and function of nucleic acids, proteins, and glycans, including the latest findings from the fields of genomics, proteomics, and glycomics. It serves as a bridge between introductory biochemistry textbooks and advanced treatises on individual classes of biomacromolecules. The integrated treatment of biomacromolecules enables the reader to gain a better understanding and appreciation of both the similarities and differences among the three classes of biomacromolecules examined in the text.


From Molecules To Medicines

Author by : Joel L. Sussman
Languange : en
Publisher by : Springer Science & Business Media
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Description : Proceedings of the NATO Advanced Study Institute on Integrating Crystallography in the Fight Against Terrorism Erice, Italy 29 May-8 June 2008


Computer Simulated Plant Design For Waste Minimization Pollution Prevention

Author by : Stan Bumble
Languange : en
Publisher by : CRC Press
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Description : Full of examples based on case studies from a variety of industries, Computer Simulated Plant Design for Waste Minimization/Pollution Prevention discusses preventing pollution and minimizing waste using computer simulation programs. The author examines the computer technologies used in the field, including the design and analysis of computer-aided flow sheets. With this book, readers will understand how to use computer technology to design plants that generate little or no pollution and how to use information generated by computer simulations for technical data in proposals and presentations and as the basis for making policy decisions.


Computer Generated Physical Properties

Author by : Stan Bumble
Languange : en
Publisher by : CRC Press
Format Available : PDF, ePub, Mobi
Total Read : 15
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Description : Computer Generated Physical Properties offers the environmental scientist a basis to predict the properties of molecules and reengineer them to remove those properties that are harmful to the environment. This technology is currently used in other fields and is now becoming popular in the environmental engineering field because of its pollution prevention and waste reduction capabilities. This book, interdisciplinary in scope, treats the physical properties of matter as generated by computers. It covers a wide variety of topics pointing towards synthesizing new molecules to substitute for reactants, intermediaries, and products in industrial processes with better physical and environmental properties than the original. The author achieves this with a spreadsheet program called SYNPROPS that operates on a PC computer with optimization features. A radar type graph - one for each property - visually sorts the various groups in order of their contribution to the property, creating the necessity for a computer to obtain answers for the structure of the optimum molecules for substitution or synthesis. The author discusses applications to biologically active molecules without side effects, including antineoplatic drugs. Additionally, he demonstrates model compounds and the applications of SYNPROPS' optimization and substitution. This book has everything you need to know about deriving properties and combinational chemistry from molecular structure.


Encyclopedia Of Nonlinear Science

Author by : Alwyn Scott
Languange : en
Publisher by : Routledge
Format Available : PDF, ePub, Mobi
Total Read : 97
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Description : In 438 alphabetically-arranged essays, this work provides a useful overview of the core mathematical background for nonlinear science, as well as its applications to key problems in ecology and biological systems, chemical reaction-diffusion problems, geophysics, economics, electrical and mechanical oscillations in engineering systems, lasers and nonlinear optics, fluid mechanics and turbulence, and condensed matter physics, among others.