Biophysics E-Book

Wayne F. Reed

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1374

Veröffentlichungsjahr: 2025

Beschreibung

An introduction to the physics of living organisms

The field of biophysics employs the principles of physics to study biological systems, and introduces the concept of the living state. It is a multidisciplinary approach to the study of the living state combining physics, biochemistry, molecular and cell biology, medicine and engineering. The physics of macromolecules and macromolecular assemblies is a particularly important aspect of this broader field.

Biophysics: Physical Processes Underlying the living state offers an introduction to the general principles of the living state and their biological applications. Beginning with an historical overview of fundamental scientific theories and fields, the book then provides a brief introduction to cell biology and biochemistry, and then an overview of basic thermodynamics, kinetics, information theory, electrostatics in solution, fluid mechanics and macromolecular physics, and their relationship to the living state. After a presentation of physical methods, with an emphasis on light scattering, different biological macromolecules, selected aspects of their functions, and their physical properties and interactions are surveyed. A brief introduction to vision, biomotion, and theoretical biology is also provided. Exploration of some frontier issues in prebiotic origins of life, consciousness, and astrobiology round out the book. The result is a multifaceted window into the broad and evolving field of biophysics.

Biophysics readers will also find:

• Problems at the conclusion of each chapter to reinforce and focus student knowledge
• A gathering of topics in basic physics and physical chemistry which are seldom found in a single source

This textbook is suitable for physics and engineering students studying biophysics, macromolecular science, and biophysical chemistry, as well as for polymer scientists, chemists, biochemists, cell and molecular biologists, bioengineers, and others.

Leseprobe

Biophysics

Physical Processes Underlying the Living State

Wayne F. Reed

Tulane UniversityNew Orleans, Louisiana, USA

Copyright © 2025 by John Wiley & Sons, Inc. All rights reserved, including rights for text and data mining and training of artificial technologies or similar technologies.

Published by John Wiley & Sons, Inc., Hoboken, New Jersey.Published simultaneously in Canada.

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, [phone], fax [phone], or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, [phone], fax [phone], or online at http://www.wiley.com/go/permission.

The manufacturer’s authorized representative according to the EU General Product Safety Regulation is Wiley-VCH GmbH, Boschstr. 12, 69469 Weinheim, Germany, e-mail: [email protected].

Trademarks: Wiley and the Wiley logo are trademarks or registered trademarks of John Wiley & Sons, Inc. and/or its affiliates in the United States and other countries and may not be used without written permission. All other trademarks are the property of their respective owners. John Wiley & Sons, Inc. is not associated with any product or vendor mentioned in this book.

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Further, readers should be aware that websites listed in this work may have changed or disappeared between when this work was written and when it is read. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at [phone], outside the United States at [phone] or fax [phone].

Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com.

Library of Congress Cataloging-in-Publication Data Applied for:

Hardback: 9781119696407ePDF: 9781119696377epub: 9781119696421

Cover Design: WileyCover Image: Created by Linnette F. Reed

Dedicated to my family, past, present, and future

Preface

Biophysics is not a canonical or settled field, unlike traditional areas of physics, such as electromagnetic theory, thermodynamics, and classical and quantum mechanics, for which a unified body of knowledge exists and is treated in approximately the same form for each subject in many different texts. All would agree that biophysics involves both physics and biology, but then perspectives, fields, and texts quickly diverge after that.

It is appealing to attempt to establish the “living state” of matter as a subspace of the vast phase diagram for multicomponent systems, which can be unified by fundamental principles: living state physics. While the living state obeys all known physical laws, there is no universal agreement about whether the currently known laws are adequate for the description of the emergence and properties of the living state, or whether there are other operative principles yet to be discovered.

Beyond the search for fundamentals, biophysics has come to encompass an enormous space of research activity at all length scales, including exoplanets, local ecosystems, macroscopic biomechanics, neuroimaging of the brain, approaches to organ function, electrophysiology, information and systems integration, cellular and membrane level functions, and structure and dynamics of biomacromolecules. Some also consider biophysics to be the transfer to life sciences of existing physical theories, such as thermodynamics, statistical mechanics, fluid mechanics, and polymer physics, and methods, such as nuclear magnetic resonance, superconducting quantum interference devices (SQUIDs), scattering techniques, and a host of optical spectroscopies, to solve biologically and medically related problems. Yet another dimension deals with the interaction of ionizing radiation with living tissue, that is, radiation biophysics. With rapid advances in neuroscience, attempts at establishing the biophysics of consciousness are underway, intense, and controversial. While quantum phenomena underlie all atomic and molecular processes, the area of quantum biology is relatively untrammeled but is quickly pushing into areas of vision, photosynthesis, enzymatic action, theories of mutation, and others.

The preface to many biophysics texts often mentions “this book grew out of lecture notes prepared while I was teaching a course in biophysics at the University.” Many biophysics instructors cannot find the constellation of topics they want to present in any single text and so weave together their own narrative. It is fascinating to peruse the wide range of available biophysics texts and see how they range from dispassionate presentations of “established fact,” to highly intuitive, integrated approaches for student discovery of principles, to mathematically dense forays into very complex, specific biological systems or functions. There is virtually no unity among biophysics texts, unlike, say, texts on classical mechanics or electromagnetism.

This work tries to capture the broad outlines of the well-understood processes and principles in the living state, while taking a more detailed look into the area of macromolecular science. No single text can adequately embrace the vast scope of knowledge in all the dimensions of the living state and macromolecular science. Virtually every topic in this book roots back to scientific developments that took centuries to establish, and for which there are entire books and even dedicated journals. Most areas are still under active investigation. As a colleague once said, “if you woke up early and studied all day long, by the end of the day the amount of new knowledge produced in the world on that day will have dwarfed what you learned.”

Regarding macromolecular science, while it is also highly interdisciplinary, the situation is more focused than for biophysics. The historical foundations of polymer research are well documented, and a certain logical flow in terms of chemical structure, reactions, and resulting properties can be established. There are well-regarded foundational texts, such as “Principles of Polymer Chemistry” by Paul Flory and “Physical Chemistry of Macromolecules” by Charles Tanford which lay out large parts of the field and continue to be relevant. Further work by researchers such as John Kirkwood, Peter Debye, Bruno Zimm, Walter Stockmayer, Hiromi Yamakawa, and Pierre-Gilles de Gennes, among many others, built the foundation for much of modern polymer physics. Hence, many of the introductory polymer science texts will follow a similar pattern while emphasizing different aspects – chemistry, physics, engineering, applications, liquid state, solid state, rheology, materials properties – according to the author’s interests.

The organization of this book is as follows:

Part I. Scientific Overview, Biological and Biochemical Surveys

Chapter 1 starts with the evolution of scientific thought and considers theories that have been successful and others that have fallen on the trash heap of discarded ideas. A fair amount of historical background is provided to give an idea of the millennia of thought and myriad of investigators behind fields, such as atomic science, evolution, and biophysics itself. There is a brief survey of the ongoing attempts to define fundamentals in biophysics, including the notion of the living state as a far from equilibrium dissipative system, in which the phenomena of self-organization, auto-catalysis, cooperativity, and information storage and processing figure largely.

Chapters 2 and 3 provide very brief overviews of biology and biochemistry, respectively, and present some of the underlying basics behind biophysics, including a condensed summary of metabolism. These chapters are intended for the physical science majors who may have had little or no exposure to these life science fields.

Part II. Physical Processes underlying the Living State

Since the living state involves chemically driven thermodynamic structures and involves the creation of order and information, principles of thermodynamics are introduced first in Chapter 4. Elementary situations are worked through to get a feel for heat flow, entropy, free energy, and chemical potential. These lead naturally to entropy-based forces, chemical kinetics, and basic nonequilibrium thermodynamics. While probability distributions and averaging recur throughout the book, no attempt is made to use statistical thermodynamics beyond the introduction of some of the most important ideas, such as the partition function and statistical interpretation of entropy. A very lean background on information theory is given, used subsequently for a simple analysis of the genetic code.

Because the living state occurs largely in aqueous phase and involves electrically charged biological molecules, attention next turns to electrostatics in solution in Chapter 5, which begins by assessing the different types of electrostatic interactions in the liquid state, including how electric potentials and ions arrange themselves around charged objects. Introductory notions of ionic equilibria across membranes are also introduced. This is followed in Chapter 6 by fluid mechanics and transport properties in solution, manifestations of which abound from the intracellular level to the largest creatures. Throughout Part II, wherever possible, the physical principles are illustrated with examples from the living state.

Part III. Macromolecular Science

The many functions of the living state are enabled by macromolecules, so considerable attention is devoted to this field. Chapter 7 provides a brief overview of important organic functional groups, along with an overview of general polymer types and properties, the polymer manufacturing industry, and details on polymerization kinetics, and macromolecular characterization methods.

There is a fascinating elision of macromolecular science and molecular biology occurring throughout the twentieth century and continuing into the current one. Accordingly, the common ground between biological and synthetic macromolecules is laid out in Chapter 8, which treats the physics of macromolecules, with an emphasis on conformations, polymer chain statistics, interactions, molar mass distributions, transport properties, and electrically charged macromolecules. To accompany the focus on macromolecules, Chapter 9 is devoted to light scattering and other scattering and optical methods for their characterization. The portion on light scattering reflects one of the author’s abiding interests, and is elaborated in detail, and subsequently used to explore a variety of processes in some of the succeeding chapters.

While the complexity and capabilities of biomacromolecules vastly surpass those of any simple, human-created polymers, the latter have still taught us many things about the mechanisms by which they are produced. A profound difference exists between the behavior of synthetic polymers acting on their own or in combination with other components in a blend or nanostructure, and the complex processes which organize, fold, stretch, edit, chemically modify, activate, and deactivate biomacromolecules performing astoundingly specialized functions.

Part IV. Examples of Specific Living State Phenomena

While Part III explored the common ground between bio- and synthetic macromolecules, biomacromolecules got a head start on Earth approximately 4 billion years ahead of the latter, and have evolved a complexity of structure and function far beyond synthetic polymers. Accordingly, Chapters 10–13 give a sampling of some of the unique properties, structures, and processes enabled by the major classes of biomacromolecules introduced in Chapter 3.

A feature of the living state that distinguishes it from nonliving forms of matter is that it is held far from equilibrium using a continuous supply of energy harvested from the environment. This permits complex, controlled dynamics, such as maintaining nonequilibrium ion gradients across membranes to produce nerve impulses, folding DNA into tiny spaces under complex 3D mechanical stresses that allows it to activate and deactivate different genetic sequences to produce proteins through feedback mechanisms, and keeping rhodopsin in an isomeric state to absorb photons and initiate the biochemical events that produce vision. Biological processes are exquisitely controlled, perhaps even optimized, and few processes proceed spontaneously. The living state is imbued with energetic cycles that allow processes to run “downhill” energetically, but then use complex mechanisms to bring the process energetically back “uphill.” Chapters 10–13 try to capture and analyze a small subset of these processes.

The many crucial living state functions of proteins, first delineated in Chapter 3, lead to Chapter 10 and the complex issue of how the amino acid sequence delivered by DNA leads to specific protein folding. This is followed by consideration of other processes, including protein aggregation, enzyme kinetics, cooperativity, phase transitions, and internal protein motions that underlie their behavior.

In Chapter 11, macromolecular properties of RNA and DNA are outlined, such as persistence length and bending energies. The genetic code is introduced and discussed in terms of information theory and protein synthesis, and the organization of DNA and associated proteins into chromatin is discussed qualitatively.

While carbohydrates might sound less glamorous than the proteins and nucleic acids, their macromolecules take on many vital functions besides their well-known energy storage. As a class of macromolecules, they can take on a wide variety of conformations, and those that are polyelectrolytes share similar physics with other charged macromolecules. An analysis of their polymer behavior in Chapter 12 is based on characterization principles from Chapter 7. Glycoproteins wed saccharides and proteins and are involved in a wide variety of signaling, immune, and control mechanisms.

Lipids, as well as the phospholipids they produce, are not in themselves macromolecules, but the principles of entropically driven self-organization and supramolecular assembly lead to the cell membrane. Chapter 13 expands on the physical properties of membranes. The membrane is a cell’s integument, its protective layer, separating it from the rest of the organism or its environment. A vast array of membrane-bound channels and receptors modulate cell functions and control interactions between the cell and its environment, including other cells. The main focus of Chapter 13 is the generation and propagation of electrical action potentials in the context of neural cell membranes.

To get a feel for how the biomacromolecules and their supporters come together to enable the living state, some integrated processes are introduced in Chapter 14. Because of the vastness of the biophysics field, I have included brief cameos of deep and fascinating areas that may whet a student’s appetite for further discovery. These include basic principles of motility, and the interaction of light with the living state, including elements of vision and image formation, several dimensions of theoretical biology, including a closer look at models of far-from-equilibrium systems, such as Turing patterns and population dynamics.

The book concludes in Chapter 15 with a glimpse of several rapidly evolving fields, including prebiotic origins of life, quantum biology, neuroscience, and exobiology. A brief survey of exoplanetary discovery is given as a crucial step in the search for extraterrestrial life.

By the end of the course, students will have at least peered through many portals onto this vast field of human endeavor. Because of the breadth and depth of the field, students can be required to make a deeper research dive into a specific area of their interest, developing a report and class presentation for the end of the semester.

W.F. Reed

January 2023

Student Audience and Particulars of This Book

This book is aimed at students at any level and field who are comfortable with basic calculus and physics. A background in basic biology and chemistry is helpful but not a prerequisite. This course has been given in various ways at Tulane University since 1986. It is normally double-listed as a graduate/undergraduate course, where the graduate students are given more challenging problems and tests to solve than the undergraduates. Students are typically graduate and undergraduate students in physics, engineering physics, chemical and biomolecular engineering, chemistry, and cell and molecular biology.

When working across disciplines, the issue of physical units can be vexing. Although the preference in this text is to use the Système International (SI), also referred to as the Meter–Kilogram–Second–Ampere system (MKSA), the physical calculations involved in aqueous solutions, the most important milieu of the living state, have traditionally been developed in the Centimeter–Gram–Second system (CGS) and the corresponding CGS Gaussian units. To strike a compromise, MKSA units will be used where traditional, e.g. in electrostatic force and potential calculations, and thermodynamic calculations (most people are used to Newtons, Joules, Volts, and Coulombs, whereas Dynes, Ergs, Statvolts, and Electrostatic Units are less familiar for most), and CGS units will be used in the traditional areas of fluid mechanics and physical chemistry of solutions … essentially, “when in Rome, do as the Romans.”

As regards notation, no attempt has been made to use the same symbols consistently throughout the book. Students are accustomed to the arbitrary nature of using symbols to represent different physical quantities and so are comfortable with adapting convenient symbols to specific situations. This avoids the use of many subscripts, boldfaces, and fonts, such as block and cursive. However, there are some quantities that are so pervasive that their symbols are always kept the same, unless otherwise noted: T = temperature, kB = Boltzmann’s constant, NA = Avogadro’s number, e = the elementary charge, and ℏ = Planck’s constant (divided by 2π).

Usage of the Book

Like many texts, this one is too lengthy to cover completely in one semester. It is suggested that the instructor identify the topics of most interest and lay down a path, incorporating as many sections as desired, while omitting portions, even whole chapters, in order to optimize its use.

Because of the vast expanse of research underway in biophysical and macromolecular areas, at the end of each chapter, there is a list of “Further Reading,” a wide selection of reviews, articles, and books, which can get the interested reader pointed in promising directions.

Part II and Chapter 9 in Part III can be used as a stand-alone course in some of the areas that traditionally receive less attention in physics curricula; fluid mechanics, scattering of electromagnetic radiation, electrostatics in solution, polymer physics, information theory, and certain less treated aspects of thermodynamics.

Acknowledgments

I thank many people for their contributions to this book. Colleagues and others who critically reviewed content and style include Dan Purrington, André Striegel, David Mullin, Larry Byers, Nick Sparks, Kathryn Stone, and Curt Jarand. Marissa Calko provided many of the figures and illustrations, while Linnette Reed created several original paintings. Sara Wrobel and Priscilla Mandujano obtained permissions for many figures.

I especially acknowledge the following students, who both took the course using a draft of this book, and who each critically reviewed several chapters: Stephen Graf, Elizabeth H. Gregory, Ben Vasquez, Brittany Kay Simone, Jackson Smith, Allen H.H. Li, Lanie McLeod, Julia S. Siqueira, and Gwen Leifer.

Support from the Murchison-Mallory Endowed Chair in physics at Tulane University is also gratefully acknowledged.

About the Companion Website

This book is accompanied by a companion website which includes a number of resources created by author for students and instructors that you will find helpful.

www.wiley.com/go/Reed/BiophysicsandMacromolecules

The instructor website includes the following resources.

• Answers to Selected Problems

Part IScientific Overview, Biological and Biochemical Surveys

1Background Notions, Histories, and Fundamental Issues in Physics and Biophysics

There is nothing quite as frightening as someone who knows they are right.

Michael Faraday

Interactions are the basis of life. For a thermodynamically “ideal” system, there is no interaction among constituents, beyond point-like elastic collisions. It is only through interaction of constituents, which is the basis of “nonideal” behavior, that phase behavior and cooperativity arise, and hence life. Nonideality manifests itself at basic levels; water freezes and boils, molten metals cool into crystals, and at advanced levels, where complex mixtures of chemicals stimulated with energy can self-organize into living structures.

1.1 The Evolution of Scientific Thought

The luminiferous aether has definite mechanical properties.

John Tyndall

Nature is reluctant to reveal her secrets. The history of science is a running drama of misconceptions seized upon as correct and final, often for centuries, before a new clarification results, itself subject to the relentless experimental tests upon which continued, provisional acceptance of scientific knowledge is based. Some of the great misconceptions in science include the geocentric theory, heat conceived as a substance called “phlogiston,” later replaced with the erroneous idea it was a fluid termed “caloric,” spontaneous generation of life, the crystalline spheres of the heavens, the luminiferous aether, absolute determinism, and many more…. One person’s theory is another’s laughingstock.

On the other hand, an imperfect theory is often perfectly adequate for some purposes and is erroneous only when pushed beyond the limits of approximation in which its validity holds. Newtonian mechanics is one of the best-known such cases, where it is valid for computing terrestrial ballistics and the greater part of planetary motion but fails dramatically on the subnanometer scale, near the speed of light, and in strong gravitational fields.

In this sense, scientific theories are maps onto physical reality, useful constructs with predictive, calculational, and manipulative power within their domain of application. While the claim is frequently made that all observable phenomena in the universe are linked to fundamental properties of matter, the existence of the living state is currently not predictable from these properties. In analogy to maps, actual map makers do not refer to distant, or even all-encompassing maps in their endeavors; making a local topographic map does not require a map of the known universe, nor could the latter predict the former. Hence, those studying chemical and biochemical reactions have no need for the current standard model of particle physics in their endeavors, nor are they stymied by our lack of understanding of cosmic dark energy and matter, even though the phenomena they study may ultimately emerge from these fundamentals.

Living state physics emerges from the fundamental properties of matter, but its manifestations seem much further removed from these fundamentals than, say, the quantum mechanical description of a molecular reaction. A current three-way split in thought (and there are more than these three) is (1) life may be viewed as perched upon a pyramid of vanishingly small thermodynamic probabilities and hence is likely quite rare throughout the universe, and (2) the opposing notion that life is actually inevitable if the right abundance of matter and energy is present under the right thermodynamic