Customer Reviews (1)

Wide-ranging and interesting
This is an awesome book, it covers a huge range of topics and shows how physical thinking can provide answers to biological questions at scales ranging from the molecular to the cellular.Most biophsics books seem to get hung up on single molecules, but this one stands out by moving beyond the simplest building blocks and discussing higher order structures, self assembly, and cell motility.The book is highly accessible and does not demand advanced prior knowledge of physics or math. ... Read more

Product Description
Chemical Biophysics provides an engineering-based approach to biochemical system analysis for graduate-level courses on systems biology, computational bioengineering and molecular biophysics. It is the first textbook to apply rigorous physical chemistry principles to mathematical and computational modeling of biochemical systems for an interdisciplinary audience. The book is structured to show the student the basic biophysical concepts before applying this theory to computational modeling and analysis, building up to advanced topics and current research. Topics explored include the kinetics of nonequilibrium open biological systems, enzyme mediated reactions, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems. End-of-chapter exercises range from confidence-building calculations to computational simulation projects. ... Read more

Customer Reviews (3)

Great
The book as in very good or better condition.With the exception of a few very minor marks which were barely visible, the book was in perfect condition.

A great book
I loved the book right from its first page to the last. Daniel and Hong have explained biophysics principle quantitatively in an easy to understand manner.

It is really a marvelous book. Essential for graduate students desiring to learn biophysical principles applied in cellular context.

Thank you Daniel and Hong for writing such a great book.

A book that fills an important gap
Almost everybody finds classical thermodynamics difficult, and this has always been so: even the great physicists of the 19th century who created the subject had to struggle to understand it. It is not so much that the mathematics is so difficult: with a proper grounding in calculus, especially partial differentiation, one can understand the equations and their derivation easily enough in mathematical terms. On the other hand the qualitative ideas of statistical thermodynamics are not so difficult either. It is the effort relating these to the mathematics, and to classical thermodynamics (heat engines, Carnot cycles, etc.) that causes the eyes to glaze over.

Unfortunately, however, a training in thermodynamics is absolutely essential to chemistry and to the chemical underpinning of the biophysical analysis of cellular systems. Metabolism, for example, is not just a matter of listing all the chemical reactions; it is also a matter of knowing which ones will readily proceed and in what conditions. Determining all this involved a great deal of measurements in the 20th century on the equilibrium constants and other thermodynamic parameters of biochemical reactions. More than that, it involved understanding how the thermodynamic parameters of whole sequences of reactions depend on those of the individual processes, and how these depend on those of the component reactants.

Until now, however, textbooks that explain the principles of thermodynamics in the biochemical context have been few, a fewer still have been written in a way that students can be expected to understand. The new book of Daniel Beard and Hong Qian fills an important gap, therefore, and should be widely adopted in all departments where physical biochemistry is taught.

The first part of the book covers the basic concepts of thermodynamics, as far as possible using biologically relevant examples. Almost immediately the authors introduce the ideas that "in biology and chemistry we are usually not interested in the study of isolated systems", and that "biochemical processes occur in an aqueous environment". This brings us quite quickly to the idea that the Gibbs energy (not the entropy, and not the Helmholtz energy) is the quantity to consider in determining the thermodynamic driving force in a typical biochemical reaction. Likewise the stress is entirely on reactions in solutions, without the emphasis on gases (whether perfect or not) that tended to characterize textbooks in the past and to mystify raeders who wondered what perfect gases had to do with the sort of processes of primary concern in biology. This part of the book also deals with basic ideas of kinetics and transport.

In the second part the authors move on to the analysis and modelling of biochemical systems, the second part of which barely existed as a research topic twenty years ago but has in recent years become an essential component of systems biology. The relationship between enzyme mechanisms and reaction kinetics is explained briefly (as this is not a kinetics book) but thoroughly, and is followed by a chapter on control mechanisms and signalling, focussing on the properties such as zero-order ultrasensitivity and biochemical oscillations that are not possible for single enzymes but can emerge from interactions between several enzymes.

The last part of the book deals with several of what the authors call special topics, mainly ones that have been mentioned already but require a more profound and detailed treatment. A chapter, for example, is devoted to constraint-based analysis of biochemical systems -- the sort of modelling one can do when there is not enough information to set up an adequate kinetic model.

In summary (as I am quoted on the back cover as saying in my report to the publishers), this is one of the most useful and readable accounts of biochemical thermodynamics that I have seen for a long time, if indeed ever. ... Read more

Product Description

This textbook offers clear explanations of the theory of optical spectroscopic phenomena and shows how these ideas are used in modern molecular and cellular biophysics and biochemistry. The topics covered include electronic and vibrational absorption, fluorescence, resonance energy transfer, exciton interactions, circular dichroism, coherence and dephasing, ultrafast pump-probe and photon-echo spectroscopy, single-molecule and fluorescence-correlation spectroscopy, Raman scattering, and multiphoton absorption.

The explanations are based on time-dependent quantum mechanics and are sufficiently thorough and detailed to be useful for both students and researchers. With the clear, thoroughly illustrated explanations that begin from first principles, the text will also be accessible to readers with little prior training in quantum mechanics. Extra details and highlights are featured in special boxes throughout the text. A helpful exercises section has been included to this new student edition.

Customer Reviews (2)

didn't help me, but might help you
Whether you'll want this book or not depends on your training and purpose.If you need a good description of the quantum mechanics of spectroscopy, buy this book.But if you're developing methods or are interested in using spectroscopy as a tool, there isn't much here to help you out.Parson's style is as follows: describe a transition in quantum mechanics terms, derive out all the physical properties of that transition (using matrices, Feynman diagrams, and operators galore), and conclude with a couple of few-sentence examples.If you "think in quantum mechanics", of course, this is a perfectly logical style.However I can't help but think this book was written for people who have to describe spectroscopy without ever actually DOING it.Instrumentation is given only a cursory once-over in the first chapter, and practical strengths and limitations (why you'd use a certain technique for a certain purpose, and what its blind spots might be) are almost totally ignored (or buried in paragraphs on selection rules).On top of that the formulaic and math-heavy text is awfully dry (it's not an "excitation laser", it's an "incident wavepacket") and there's a sameness to the chapters that makes it a chore to read.It's nice to have a handy reference on the quantum mechanics, but for an applications-oriented person like myself there is not much practical in this book.

20/20 Vision For Theoretical Treatment of Optical Spectroscopy
As a biochemist who uses electronic spectroscopy as a tool for solving biochemical problems I have come to appreciate certain deficiencies in my academic training.Aspects of quantum mechanics and molecular orbital theory that are not normally a core part of biochemistry curricula are clearly important for understanding and interpreting experimental findings obtained by spectroscopic methods such as ultraviolet absorbance and circular dichroism.Perhaps the most useful text that I've found to help me come to grips with the subject is the 1962 classic "Theory and Applications of Ultraviolet Spectroscopy," by Jaffé and Orchin.Here the focus is on organic chemistry, but William W. Parson has now provided a deeper treatment of the theory that draws examples from biophysics and biochemistry.Parson has filled in the many gaps that appear to have emerged in the discipline in the past 45 years.For me it has been a revelation to see explanations from first principles for the origins of the Rosenfeld equation and the point-dipole approximation, for example.Parson makes an interesting connection between Förster and exciton theories as variations on a common theme of excited state delocalization, but at greater and shorter distances, respectively.One criticism is that the discussion of the exciton effect seems to be limited entirely to the degenerate case where chromophores having identical energies interact.I would like to have seen the non-degenerate case discussed as Harada and Nakanishi treated it previously in Chapter 10 of their treatise on circular dichroism.I have not had a chance to read Parson's entire book, but what I have consulted has been gripping and easy to comprehend - the appendices on vectors, matrices, and Fourier transforms have certainly helped me to overcome some of my own deficiencies with the mathematics.Ultimately, Parson strives to create a physical picture that mathematics only serves to summarize, which is precisely what I want to know.I suspect that "Modern Optical Spectroscopy" will become an essential reference for experimentalists who seek to be quantitative in interpreting their observations derived from a wide range of electronic spectroscopic methods. ... Read more

Product Description
This newly revised and updated edition of Radiation Biophysics provides an in-depth description of the physics and chemistry of radiation and its effects on biological systems. Coverage begins with fundamental concepts of the physics of radiation and radioactivity, then progresses through the chemistry and biology of the interaction of radiation with living systems. The Second Edition of this highly praised text includes major revisions which reflect the rapid advances in the field. New material covers recent developments in the fields of carcinogenesis, DNA repair, molecular genetics, and the molecular biology of oncogenes and tumor suppressor genes. The book also includes extensive discussion of the practical impact of radiation on everyday life.

Key Features
* Covers the fundamentals of radiation physics in a manner that is understandable to students and professionals with a limited physics background
* Includes problem sets and exercises to aid both teachers and students
* Discusses radioactivity, internally deposited radionuclides, and dosimetry
* Analyzes the risks for occupational and non-occupational workers exposed to radiation sources ... Read more

Customer Reviews (2)

Inadequate "Bio" in the "Biophysics"
The major book on radiation biology / radiation biophysics has been Hall's "Radiobiology for the Radiologist" now in it's 5th edition.It would be nice to have an alternative to this, particularly since that one is so weighted toward radiation oncology and radiology.Alpen's"Radiation Biophysics" (1998, 2nd ed.) tries to be a more general alternative, but it fails because of some glaring omissions and a level of biological sophistication that is at least 15-20 years out of date.Here are a few examples.

- Although the revolutions in molecular biology and in signal transduction were late in penetrating the field of radiation biology, this kind of information has made its way into other texts but it is largely absent and mishandled in Alpen's book.While p53 is pitiably mentioned (an engineer or physicist is unlikely to understand Alpen's textual description, a diagram would have been more useful to cut through the jargon), absent are important regulators like ATM, Rb, and egr-1, and a mechanistic description of how all this fits in together.
- Woefully brief and out of date is Alpen's discussion on biological modifiers of radiation sensitivity, e.g., the chemical WR2721 is described as having "limited value," citing studies from 1980, but this drug (also known as Amifostine) is in current clinical use today (2003) for radiation therapy of head & neck cancer and other tumors.In addition, missing is a decade of work on growth factors and cytokines that act as radiation protectors and radiation sensitzers.
- While other books devote an entire chapter to the "oxygen effect," Alpen devotes only couple pages to this topic, failing to discuss how hypoxia (low dissolved oxygen concentration) in tissues makes them radioresistant.
- While other books devote entire chapters to how the cell cycle influences radiation sensitivity, Alpen devotes only one and half paragraphs to this topic.
- Discussion of the biological basis of "fractionation" is totally inadequate.This is where radiation exposure is broken up a little bit at a time, in relatively small doses spread out over a longer period, rather than at a high dose all at once. The ultimate extension of this is something called "brachytheraphy" which gives local, continuous low dosing by implanting "radioactive seeds" right into a tumor.Brachytherapy has emerged as a common treatment for prostate cancer, for example.Conceptually, brachytherapy ties in several aspects of radiation biophysics, including the use of radioactive isotopes, but it is nowhere to be found in this book.

While Alpen does a reasonably good job at describing physical phenomena and at deriving equations, and the book is very well-written, the shallowness ofbiological information really hurts the overall effort.If one is interested in a book purely devoted to radiation physics, Khan's 1994"The Physics of Radiation Physics" should be considered.However, anyone interested in books that REALLY cover the biological background in great detail should get Travis' 1989 "Primer of Medical Radiobiology" which is still in its 2nd edition but is nevertheless fine for it's strong, classic biomedical emphasis (the modern stuff will undoubtedly appear in the 3rd edition, which is still in the works), or again, go to Hall's very well-rounded classic.

An excellent introduction to Radiation Biophysics
This is an excellent book which everyone interested in radiation biophysics must have have read. The book has 16 chapters. In the first 6 the emphasis is on physics. In the following 10 chapters, the models forcell survival and the effect of radiation on tissue structures andorganisms are discussed in great detail. A must for anyone interested inand trying to understand the "biological" background of radiationprotection and radiotherapy. ... Read more

Product Description

This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including quantum photonics of organic dyes and inorganic nanoparticles and monitoring of single molecule (enzymatic) reactions.

Product Description

The book contains lectures of an international NATO-Russian Advanced Workshop about the detection of liquid explosives and flammable agents. The ARW was one of a series of workshops before, dealing with the detection of explosives and initiated by terrorist actions using liquid explosives. The aim of the workshop was to present and to discuss suitable methods about the feasibility and realization of the detection of liquid explosive charges and flammable agents.

Product Description
This book presents the fundamentals of molecular biophysics, and highlights the connection between molecules and biological phenomena, making it an important text across a variety of science disciplines.

The topics covered in the book include:

• Phase transitions that occur in biosystems (protein crystallisation, globule-coil transition etc)
• Liquid crystallinity as an example of the delicate range of partially ordered phases found with biological molecules
• How molecules move and propel themselves at the cellular level
• The general features of self-assembly with examples from proteins
• The phase behaviour of DNA

The physical toolbox presented within this text will form a basis for students to enter into a wide range of pure and applied bioengineering fields in medical, food and pharmaceutical areas.

... Read more

Customer Reviews (1)

Really Bad - Don't buy, its a waste of money
Having entered this field of research recently I was looking for standard literature in the field of Computational Biophysics and stumbled upon this book by Waigh.
Well, in my judgement, it is mediocre as a textbook. The author is apparently a physicist that doesn't know much, if at all, of biophysics and biochemistry. This isn't necessarily bad for writing a textbook on Applied Biophysics, but the book doesn't keep its promise, because the author has no experience in biophysics really which you tell from the choice of chapters and the topics covered. Most likely he is a physicist that at some point entered the field of polymer or biophysics. The usual stuff: Crystallinity, self-Assembly, polymer dynamics, Scattering theory, diffusion, surfactants, rheology, electrostatics, capilarity, all the stuff that you can find in so many other textbooks and which he probably only had to copy and then maybe draw some new figures. This is a introductory first semester course in polymer physics. But as such, there are many better books on the field on the market, e.g. Polymer Physics by Rubinstein and Colby who offer much more detailed and knowledgable insight into these topics than Waigh. As an alibi, there is ONE chapter on DNA at the end of the book and one on membranes. But these cover extremly shallow only the very basics that you find in any introductury biology or molecular biology textbooks. Probably the author himself read such chapters in other books for the first time when he wrote his own book.
The first chapter on proteins is extremely shallow, superficial and unspecific. No real theories are explained or expanded on, no computational models, not a single algorithm, nothing that goes into any detail or would be helpful for someone trying to start research in this field. This book strikes me as being written by someone who just wanted to write a book that "sounds" interesting by the title. In my opinion this book is completely superfluous, it doesn't cover any advanced topics, there is nothing new, just a conglomerate of basics which you can find in so many other books that have been already on the market for years. As a physicist, the author is also not an expert in this field. Very dissapointing. I don't recommend it and I regret having wasted my money. I rather invest my money now in trying to read original research papers in this field, particularly on simulation models, written by experts who really do research in this area and publish their own, original ideas. ... Read more

Product Description
(Narosa Publishing House) Univ. of Madras, Chennai, India. Addresses the needs of biologists, biochemists, and medical biophysicists as an introduction to the subject. Based on a graduate one-semester course. Covers topics from quantum mechanics to pre-biotic evolution. ... Read more

Product Description
An overview of recent experimental and theoretical developments in the field of the physics of membranes, including new insights from the past decade.

The author uses classical thermal physics and physical chemistry to explain our current understanding of the membrane. He looks at domain and 'raft' formation, and discusses it in the context of thermal fluctuations that express themselves in heat capacity and elastic constants. Further topics are lipid-protein interactions, protein binding, and the effect of sterols and anesthetics. Many seemingly unrelated properties of membranes are shown to be intimately intertwined, leading for instance to a coupling between membrane state, domain formation and vesicular shape. This also applies to non-equilibrium phenomena like the propagation of density pulses during nerve activity.

Also included is a discussion of the application of computer simulations on membranes.
For both students and researchers of biophysics, biochemistry, physical chemistry, and soft matter physics. ... Read more

Product Description
This book is dedicated to the multiple aspects, that is, biological, physical and computational of DNA and RNA molecules. These molecules, central to vital processes, have been experimentally studied by molecular biologists for five decades since the discovery of the structure of DNA by Watson and Crick in 1953.Recent progresses (e.g. use of DNA chips, manipulations at the single molecule level, availability of huge genomic databases...) have revealed an imperious need for theoretical modelling. Further progresses will clearly not be possible without an integrated understanding of all DNA and RNA aspects and studies.

The book is intended to be a desktop reference for advanced graduate students or young researchers willing to acquire a broad interdisciplinary understanding of the multiple aspects of DNA and RNA. It is divided in three main sections:

The first section comprises an introduction to biochemistry and biology of nucleic acids. The structure and function of DNA are reviewed in R. Lavery's chapter. The next contribution, by V. Fritsch and E. Westhof, concentrates on the folding properties of RNA molecules. The cellular processes involving these molecules are reviewed by J. Kadonaga, with special emphasis on the regulation of transcription. These chapters does not require any preliminary knowledge in the field (except that of elementary biology and chemistry).

The second section covers the biophysics of DNA and RNA, starting with basics in polymer physics in the contribution by R. Khokhlov. A large space is then devoted to the presentation of recent experimental and theoretical progresses in the field of single molecule studies. T. Strick's contribution presents a detailed description of the various micro-manipulation techniques, and reviews recent experiments on the interactions between DNA and proteins (helicases, topoisomerases, ...). The theoretical modeling of single molecules is presented by J. Marko, with a special attention paid to the elastic and topological properties of DNA. Finally, advances in the understanding of electrophoresis, a technique of crucial importance in everyday molecular biology, are exposed in T. Duke's contribution.

The third section presents provides an overview of the main computational approaches to integrate, analyse and simulate molecular and genetic networks. First, J. van Helden introduces a series of statistical and computational methods allowing the identification of short nucleic fragments putatively involved in the regulation of gene expression from sets of promoter sequences controlling co-expressed genes. Next, the chapter by Samsonova et al. connects this issue of transcriptional regulation with that of the control of celldifferentiation and pattern formation during embryonic development. Finally, H. de Jong and D. Thieffry review a series of mathematical approaches to model the dynamical behaviour of complex genetic regulatory networks. This contribution includes brief descriptions and references to successful applications of these approaches, including the work of B. Novak, on the dynamical modelling of cell cycle in different model organisms, from yeast to mammals.

. Provides a comprehensive overview of the structure and function of DNA and RNA at the interface between physics, biology and information science. ... Read more

Product Description

Metamaterials and plasmonics are cross-disciplinary fields that are emerging into the mainstream of many scientific areas. Examples of scientific and technical fields which are concerned are electrical engineering, micro- and nanotechnology, microwave engineering, optics, optoelectronics, and semiconductor technologies. In plasmonics, the interplay between propagating electromagnetic waves and free-electron oscillations in materials are exploited to create new components and applications. On the other hand, metamaterials refer to artificial composites in which small artificial elements, through their collective interaction, creates a desired and unexpected macroscopic response function that is not present in the constituent materials.

This book charts the state of the art of these fields. In May 2008, world-leading experts in metamaterials and plasmonics gathered into a NATO Advanced Research Workshop in Marrakech, Morocco. The present book contains extended versions of 22 of the presentations held in the workshop, covering the general aspects of the field, as well as design and modelling questions of plasmonics and metamaterials, fabrication issues, and applications like absorbers and antennas.

Product Description
Biological chemistry has changed since the completion of the human genome project. There is a renewed interest and market for individuals trained in biophysical chemistry and molecular biophysics.The Physical Basis of Biochemistry, Second Edition, emphasizes the interdisciplinary nature of biophysical chemistry by incorporating the quantitative perspective of the physical sciences without sacrificing the complexity and diversity of the biological systems, applies physical and chemical principles to the understanding of the biology of cells and explores the explosive developments in the area of genomics, and in turn, proteomics, bioinformatics, and computational and visualization technologies that have occurred in the past seven years. The book features problem sets and examples, clear illustrations, and extensive appendixes that provide additional information on related topics in mathematics, physics and chemistry. ... Read more

Customer Reviews (3)

Messy Failure
Concept-wise, the physics in the book is superficial, often fuzzy, sometimes plain wrong. (As a simultaneous example of the latter two, just read a paragraph allegedly explaining why atomic orbitals of the wrong symmetry do not contribute to a given molecular orbital. The author hardly knows simple group-theoretical explanation, so he provides nebulous metaphysical fertilizer instead). IMHO, the author merely does not understand physics well enough to help reader's understanding.

References to nonexisting equations (e.g. Eq. 6.104 in Chapter 6), numerous numerical errors (e.g. to convert answer from Joules to calories, the author multiplies (rather than divides) by 4.2, "typos" like C(n,n)=0 instead of C(n,n)=1,and other types of sloppiness do not help either.

I had much better luck with Nelson's
"Biological Physics : Energy, Information, Life" - much more instructive and insightful exposition, which reads like a strenuous hike over a beatiful terrain

A bad book with good intentions
The author attempted to write the Feynman's Lectures of biophysical chemistry, but he failed miserably. The book has a messy structure, unclear discussions, poorly drawn diagrams, and is infested with errors, even inequations that belong to high-school level physics courses. The first thirdof the book is basically a review of freshman physics and hardly touchesbiological systems, while the rest is a combination of dry formalexposition of thermodynamics and kinetics, and overly philosophicalabstract and qualitative discussion of biological systems. The three partsof the text fail to communicate as they should.

Although I doubt thatanyone will benefit much from this book, I am sure that many biochemistrystudents would benefit greatly from a book that Dr. Bergethon actuallyWANTED to create. Until such a book appears, for physical basis ofbiochemistry buy "Physical Chemistry: Principles and Applications inBiological Sciences" by T inoco, Sauer and Wang and supplelent it withany of the better introductroy physics texts.

One professor's opinion
I bought this book just before teaching Physical Chemistry. It started with a strong development of model use which laid a strong foundation for the remainder of the book. I found it a pleasure to read, if one canimagine that in a p-chem book. A true physical chemist would find theirtreatment an oversimplification. I thought it was a great single step upfrom undergraduate biochemistry courses towards physical chemistry. ... Read more

Product Description
The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market.

It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins.

The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including color illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership. ... Read more