Understanding Molecular Simulation (Computational Science Series, Vol 1)

Book Description

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.

Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on:

· Transition path sampling and diffusive barrier crossing to simulaterare events
· Dissipative particle dynamic as a course-grained simulation technique
· Novel schemes to compute the long-ranged forces
· Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations
· Multiple-time step algorithms as an alternative for constraints
· Defects in solids
· The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules
· Parallel tempering for glassy Hamiltonians

Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Customer Reviews:

great book for MD basics.......2007-05-07

I was especially delighted about the Monte Carlo methods and the free energy calculation techniques.

Old fashioned fortran, strong bias on Monte Carlo.......2006-06-19

There is a very strong bias to MC methods in the book. What they have to say about Molecular Dynamics methods is not really new, most of it is virtually copied from the classic by Allan/Tildesley, and many MD techniques which they consider "advanced" (such as cell list methods, verlet tables, etc.) are shifted to one of the many appendices. They do not talk about ghostparticles for instance or give a detailed account of parallelized algorithms which is really state-of-the art today.
The code examples for download for the exercises, contain subtle errors, are not optimized for performance (which is THE most important thing in simulation business) and worst of all, are written in Fortran. The fact that they publish Fortran code must reflect the fact that at the time they learned how to program a computer there was no C, C++, JAVA, etc. and no object orientation in sight. Nowadays, probably no expert in programming would start a scientific and readable code in fortran. Also their definition of an algorithm is simply technically wrong. The authors are very sloppy here, have obviously no training in theoretical computer science and are obviously no experts for writing optimal code.
Scientifically, as far as physics is concerned, the book is sound, they give good arguments pro and against certain methods, but when you have already worked with Allan/Tildesley or Rappaport for many years you have the eery impression that they simply repeat many arguments from these books or from other research articles (They keep citing Allan/Tildesley a lot) Those things that are not more or less copied from other sources seems to reflect their own experience in this field which seems to be strongly limited to MC methods.
Although this book is sometimes praised I cannot really recommend it. Allan/Tildesley, and in particular the book by Rappaport are superior in stlye and in particluar as code examples are concerned. With Rappaport you get working code right away in proper C (albeit in Fortran-Style C -- again, the reason for this being the fact, that all these authors of Simulation books learned programming probably in the late 70's when Fortran was state-of-the-art). I nevertheless would recommend Rappaports book instead. The authors even offer scientific workshops based on their book (and probably make a lot of money with that). One can only hope that those are better than the coding examples of the exercises. Therefore only 2 stars.

Excellent text for beginners in simulation.......2004-11-20

Its an excellent book for those who are just beginners in MC & MD simulations. everything is very clearly explained with lot of examples and some related unsolved problems. the text explores this topic indetails with advanced chapters in later sections. Good for anybody int hsi field be it in materials science, physics or related fields.

Perfect for New Grad Students.......2002-11-24

This book is how I bootstrapped my way into being a molecular simulationist. Anyone who can program in some language can get started writing simple routines for the basic MD and MC simulations.

I do Monte Carlo simulations at Princeton, and found this book to be the most helpful available for getting my research started. It is my most common reference, and is used extensively in writing background information for various research documents.

However, after you have written your first few codes, you will pass the level of this book and need to move on. I use it less now than I did my first year.

Every student in my group (Panagiotopoulos) has this book I think. And like me, they started with it, but moved on.

A nice disappointment.......2001-08-30

The title of the book is overly ambitious and falls short on its promises. The book is a good introduction to Molecular Mechanics (MM), Molecular Dynamics (MD) and Monte Carlo (MC) methods, with detailed descriptions of the methods used and FORTRAN (pseudo)code, covering from the basics to some middle-level and some advanced algorithms.
But it does NOT cover all the fields of Molecular Modelling, just the three mentioned (MM, MD and MC), there's no coverage of quantum mechanics methods, nor QSAR or other technologies. And, while it described the algorithms, I can't think of it going all the way through up to building applications. For this, Rapaport's makes a better job, and for a general intro to Molecular Modelling, Grant & Richards' Computational Chemistry is more comprehensive (albeit at a more superficial level). Nor does it provide much detail on the methods used in modelling biological macromolecules, an increasing application field for the methods discussed in the book.
All in all, this book fails to satisfy its cover title, it won't introduce to the whole field (just the areas of MM, MD and MC) nor does it go up to application level. But it IS a REAL GOOD introduction to the subjects covered and their basic algorithms,
with sample code, detailed descriptions and plenty of references to specialized articles, texts and resources.

Principles of Physical Chemistry: Understanding Atoms, Molecules and Supramolecular Machines

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Yes, this is really an entirely fresh start for P-Chem!
The first fully coherent, continuous and truly modern text!

Principles of Physical Chemistry: Understanding Atoms, Molecules and Supramolecular Machines
Hans Kuhn , and Horst-Dieter Försterling
Manufacturer: Wiley
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471959022

Book Description

"This admirable text provides a solid foundation in the fundamentals of physical chemistry including quantum mechanics and statistical mechanics/thermodynamics. The presentation assists the students in developing an intuitive understanding of the subjects as well as skill in quantitative manipulations. Particularly exciting is the treatment of larger molecular systems. With a firm but gentle hand, the student is led to several organized molecular assemblies including supramolecular systems and models of the origin of life. By learning of some of the most productive areas of current chemical research, the student may see the discipline as an active, young science in addition to its many accomplishments of earlier years. This text makes physical chemistry fun and demonstrates why so many find it a stimulating and rewarding profession."
Professor Edel Wasserman, President (1999) of the American Chemical Society

Customer Reviews:

Yes, this is really an entirely fresh start for P-Chem!.......2000-07-29

This is, as Dr Bassi points out, really a new and modern book. It starts with Q.M. and introduces only formulas that are simple enough to be able to find use throughout the rest of the text. The whole book is just so coherent! The author knows all the time what you know, from following his book carefully, and pushes you all the time to your limit - but not beyond, as the mathematical derivations really are "neat". All other books are broken up into three major parts, between which there is only superficial connection. Here, the same equations govern every concept touched upon. It gives you a great feeling of satisfatcion and understanding! Overall, the book feels more like a novel, for its exciting style of writing and, again, continuity! (In spite of using very few words - this is definitely not the work of a graphoaniac!) If this is a textbook, then it sure is one of an all new breed... I look forwards to the next edition, with better binding and fewer misprints. And perhaps a supplementary volume with excercises, too. Get this book now! Even if you know this stuff, following the golden threads that the authors lay out, in a very personal and novel way, might let you experience some connections anew, or at least test your own skill agianst some unusual conclusions that pop ur here and there.

The first fully coherent, continuous and truly modern text!.......2000-07-21

By Giovani_Bassi@Hotmail.com

This book is really, really new in its disposition. I admire that someone still has courage to follow his (or hers) own ideas, instead of just going with established trends, that are not necessarily very good. The authors are brilliant scientists, and the sharpness of their intellects and their passion is with you all the time. I must again be very brief, but can give the following comments on this masterpiece:

- The authors accomplish "the impossible": the book allows the reader to refer to individual chapters - as reference, then, thanks to very lucid, simple mathematical derivations, always with the weaknesses in the models used clearly defined - as well as to read the entire book and "survive" - i.e. understand what one is reading - without using any other sources parallel.

- The authors start with defining the few q.m. notions, very simply and lucidly, that are then used throughout the book (modern as it is!), rather than using the archaic introduction comprised of abstract classical-thermodynamic discussions, that set out to uselessly "reinvent the wheel", by refusing to take help of the fact that we know about the discontinuity of matter (i e atoms). No more q.m. is presented than that which is needed in the rest of the book, otherwise a great danger to coherence, in my opinion (a disesase of most modern "phone-directory texts"). And this is typical of the book: no more is introduced than that which is needed - and then, those concepts are used throughout, afterwards, which is wonderful for the user: it both lets him experince control and also is the best sort of review, to actually use the concepts learned.

- Almost every theory presented is immediately afterwards applied to actual, down-to-earth chemistry, always involving familiar undergraduate topics, mostly from organic and biochemistry. Again, this is valuable as review for this courses and further reflection. Note that the examples are always VERY, VERY INTERESTING.

- As indicated, the book presents one whole, unified view, and what will be to the immense joy of all students, these authors point out, carefully, whenever something is observed that should be surprising (surprising to all those that are not already post-doctors in this area; again a stupid habit in other books of the "anthology" variety, like Atkins, Moore..., that just give you a wild array of topics, naturally RELATED, but in the books only slightly CONNECTED). Actually, often an observation is first presented, and then the situation is investigated - very beautiflly and simply.

- More advanced material is collected in boxes, but is still referred to, at later times, when appropriate.

- The authors have taken much trouble in presenting some "science philosophy", asking you to become aware of your own thinking process, and even questioning the habit of assuming correctness of our mind. I just love this.

- The introduction to Supramolecular Machines is extremely fascinating, BUT although it acts as a "carrot" for the reader to get through the earlier chapters, it is not so strongly connected with the rest of the book that it deserves mentioning in the title itself. I see this as "advertising" on the part of the authors for this area - which I do not criticize. This area (hard to define!) might well become as important as biotechnology.

Book Description

There are many different types of explosions, each with its own complex mechanism. Understanding explosions is important in preventing them. This reference provides valuable information on explosions for everyone involved in the operation, design, maintenance, and management of chemical processes, helping enhance understanding of the nature of explosions and the practical methods required to prevent them from occurring.

The text includes:

Fundamental basis for explosions
Explosive and flammable behavior and characteristics of materials
Different types of explosions
Fire and explosion hazard recognition
Practical methods for preventing explosions or minimizing the potential consequences
Additional references

Understanding Explosions provides a practical understanding of explosion fundamentals, including the different types of explosions, the explosive and flammable behavior of materials, and the hazards related to fires and explosions. It also discusses practical methods to prevent and minimize the probability and consequence of an explosion during routine use of flammable, combustible and/or reactive materials.

Understanding Drug Release and Absorption Mechanisms: A Physical and Mathematical Approach

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Understanding Drug Release and Absorption Mechanisms: A Physical and Mathematical Approach
Mario Grassi , Gabriele Grassi , Romano Lapasin , and Italo Colombo
Manufacturer: CRC
ProductGroup: Book
Binding: Hardcover

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ASIN: 0849330874

Book Description

Demand for better reliability from drug delivery systems has caused designers and researchers to move away from trial-and-error approaches and toward model-based methods of product development. Developing such models requires cross-disciplinary physical, mathematical, and physiological knowledge. Combining these areas under a single cover, Understanding Drug Release and Absorption Mechanisms builds a firm understanding of all elements needed to conceive, build, and implement successful models of drug release. Written by experts with broad industrial and academic experience, this book discusses the underlying physical principles, shows how to build mathematical models based on these principles, and finally compares the resulting models with experimental results. The authors begin by introducing the basics of modeling, physiological details of gastrointestinal and dermal absorption pathways, rheology, mass transport and thermodynamics, dissolution and partitioning, as well as size effects on the dissolution of crystallites. From this baseline, the authors explore applications in drug release from various delivery systems, specifically matrix systems, microemulsions, and permeability through membranes. Working systematically from theory to working models, Understanding Drug Release and Absorption Mechanisms: A Physical and Mathematical Approach demonstrates the steps involved in designing, building, and implementing realistic and reliable models of drug release without unrealistically simplifying the theoretical parameters.

Understanding Solids: The Science of Materials

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Book Review
A textbook both deep and extensive on Materials Chemistry

Understanding Solids: The Science of Materials
Richard J. D. Tilley
Manufacturer: Wiley
ProductGroup: Book
Binding: Paperback

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Materials Science and Engineering: An Introduction
Introduction to Physical Polymer Science
$Elements of X-Ray Diffraction (3rd Edition)$ Elements of X-Ray Diffraction (3rd Edition)

ASIN: 0470852763

Book Description

A modern introduction to the subject taking a unique integrated approach designed to appeal to both science and engineering students. Covering a broad spectrum of topics, this book includes numerous up-to-date examples of real materials with relevant applications and a modern treatment of key concepts. The science bias allows this book to be equally accessible to engineers, chemists and physicists.
* Carefully structured into self-contained bite-sized chapters to enhance student understanding
* Questions have been designed to reinforce the concepts presented
* Includes coverage of radioactivity
* Relects a rapidly growing field from the science perspective

Download Description

A modern introduction to the subject taking a unique integrated approach designed to appeal to both science and engineering students. Covering a broad spectrum of topics, this book includes numerous up-to-date examples of real materials with relevant applications and a modern treatment of key concepts. The science bias allows this book to be equally accessible to engineers, chemists and physicists. Carefully structured into self-contained bite-sized chapters to enhance student understanding Questions have been designed to reinforce the concepts presented Includes coverage of radioactivity Relects a rapidly growing field from the science perspective

Customer Reviews:

Book Review.......2006-03-20

This is a good book overall covering many areas of the science of solids. More specifically from the nuclear level through phase diagrams, crystallography, metals, chemical reactions and physical properties. It is recommended for people with a grounding in these areas and is good up to college level. It is also suitable for those (like me) who wish to refresh their memories. It has been well reviewed by at least one scientific journal that I have seen. A very good book.

A textbook both deep and extensive on Materials Chemistry.......2006-01-30

One major problem in introductory books to Materials Chemistry and Physics is how large the subject is. The rampant growth of new materials and their applications makes any textbook obsolete in a couple of years. R. J. D. Tilley put together a modern and thorough book that students (and instructors) will enjoy. The explanations of the theory are clear and rigorous enough. All graphs are truly self-explanatory. However, this is also the book
weak point. Some of those plots use lines too thin, which may affect people with visual difficulties. Last but not least, the softcover edition is quite affordable, which is not surprising from this publisher truly committed to physical science education.

Practical Dispersion: A Guide to Understanding and Formulating Slurries

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Practical Dispersion: A Guide to Understanding and Formulating Slurries
R. F. Conley
Manufacturer: Wiley-VCH
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471186406

Book Description

Practical Dispersion A Guide to Understanding and Formulating Slurries Robert F. Conley This book is a practical guide to producing slurries more efficiently, intelligently, and economically. It provides hands-on knowledge of sufficient technical depth to allow those personnel involved in on-going dispersion practices to feel more proficient in making system modifications, as well as to meet the specific mechanical, chemical, environmental, and other requirements of their customers. To this end, a broad description of dispersants, their functions, and field applications has been provided. Dispersant activities are defined on the basis of solid and agent structures and affinities. This book is intended for technical personnel in the many industries involved with slurry processing either in materials production or application, and whose day-to-day activities lie in manufacturing such dispersed products as paints; pigment premixes; treated metallic, inorganic, and organic powders; food products; cosmetics; pharmaceuticals; and dyes and inks.

A Practical Guide to Understanding the NMR of Polymers

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A Practical Guide to Understanding the NMR of Polymers
Peter A. Mirau
Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471371238

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A Practical Guide to Understanding the NMR of Polymers presents an introduction to the theory and practice of NMR, and includes sections on the fundamental principles of NMR and the applications to polymers. This book will help readers understand how these methods can be used to determine the chemical structure of polymers that influences the macroscopic properties. Solid state NMR methods are introduced to enable the readers to measure the structure of polymers on longer length scales. It is also shown how NMR is used to measure the molecular dynamics that can be related to the mechanical properties of polymers.

Physical Chemistry: Understanding our Chemical World

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It is what it is
Good for a low level intro course

Physical Chemistry: Understanding our Chemical World
Paul M. S. Monk
Manufacturer: Wiley
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Binding: Paperback

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ASIN: 0471491810

Book Description

Aimed at undergraduate students taking a first course in physical chemistry, this book offers an accessible applications/examples led approach to enhance understanding and encourage and inspire the reader to learn more about the subject.

A comprehensive introduction to physical chemistry starting from first principles.
Carefully structured into short, self-contained chapters.
Introduces examples and applications first, followed by the necessary chemical theory.

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Understanding Physical Chemistry is a gentle introduction to the principles and applications of physical chemistry. The book aims to introduce the concepts and theories in a structured manner through a wide range of carefully chosen examples and case studies drawn from everyday life. These real-life examples and applications are presented first, with any necessary chemical and mathematical theory discussed afterwards. This makes the book extremely accessible and directly relevant to the reader. Aimed at undergraduate students taking a first course in physical chemistry, this book offers an accessible applications/examples led approach to enhance understanding and encourage and inspire the reader to learn more about the subject. A comprehensive introduction to physical chemistry starting from first principles. Carefully structured into short, self-contained chapters. Introduces examples and applications first, followed by the necessary chemical theory.

Customer Reviews:

It is what it is.......2006-06-10

This book is everything it says it is. I am in school to be a chem teacher and P chem has been mind boggling. The many examples gets a person into thinking like a p chemists and this is invaluable when trying to set up the math problems in an acutal class. If you understand your Calc the math isn't the issue in passing p chem its setting up the math. This book is a must read for any under grad chemist. I am going to write the author this book is a master piece. Simple and to the point with lots of real world examples.

Good for a low level intro course.......2006-04-21

This book does a great job at discribing the conceptual aspects of basic p.chem topics like thermodynaics, kinectics and photochemistry. Unfortuently it only breafly explaines the mathmatical aspects and in little detail, making the book unsutible for anythig except a low level class. The book also suffers from a severe lack of practice problems. If you only need to understad the basic concepts of p.chem this book cannot be beat, but if you need to know the nitty gritty mathmatical deatials you will be hurting at test time.

Homogeneous Catalysis: Understanding the Art

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Homogeneous Catalysis: Understanding the Art
P.W. van Leeuwen
Manufacturer: Springer
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The Organometallic Chemistry of the Transition Metals, 4th Edition

ASIN: 1402031769

Book Description

Homogeneous Catalysis: Understanding the Art gives real insight in the many new and old reactions of importance. It is based on the author's extensive experience in both teaching and industrial practice. Each chapter starts with the basic knowledge and ends with up-to-date concepts. The focus of this book is on concepts, but many key industrial processes and applications that are important in the laboratory synthesis of organic chemicals are used as examples. The full range of topics is covered, such as fine chemicals, bulk chemicals, polymers, high-tech polymers, pharmaceuticals, but also important techniques and reaction types among other aspects. For a few reactions the process schemes, environmental concerns and safety aspects are included, to encourage catalyst researchers to think about these topics at an early stage of their projects and to communicate with chemical engineers, customers and the end-users. Homogeneous Catalysis: Understanding the Art provides a balanced overview of the vibrant and growing field of homogeneous catalysis to chemists trained in different disciplines and to graduate students who take catalysis as a main or secondary subject. This book is an invaluable tool for practising professionals and academia, including: Chemists in academia with an inorganic, organic, catalytic, etc., chemistry background; PhD-students in these fields, and advanced students;Research Institutes of Petrochemical industries; Fine-chemical industries; Pharmaceutical industries; Chemical Laboratories of Universities for Organic, Industrial, Inorganic, and Physical Chemistry, and Catalysis; Graduate schools. There is no other book available that gives insight into so many reactions of importance, while the field of homogeneous catalysis is becoming more and more important to organic chemists, industrial chemists, and academia. This book will provide this background to chemists trained in a different discipline and graduate and masters students who take catalysis as a main or secondary topic.

Organometallic Ion Chemistry (Understanding Chemical Reactivity)

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Organometallic Ion Chemistry (Understanding Chemical Reactivity)

Manufacturer: Springer
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Binding: Hardcover

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Organometallic Ion Chemistry features eight chapters, written by acknowledged authorities, covering the gas-phase chemistry of organometallic ions. Topics covered include: periodic trends in gas-phase thermochemistry of transition metal-ligand systems; ab initio calculations to determine electronic structure, geometric structure, and thermochemistry of metal-containing systems; electronic state effects on metal ion reactivity; organometallic ion photochemistry; applications of gas-phase electron transfer equilibria in organometallic redox thermochemistry. Also included are state of the art mass spectrometric instrumentation used in such studies. Finally, the book features - for the first time in one place - a comprehensive list (containing over 1500 entries) of metal ion-ligand bond energies, obtained from theory and experiment. An invaluable reference source for ion chemists, organometallic chemists and surface chemists, at both expert and graduate student levels.

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