Physics of the Life Sciences

Transcription

1 Physics of the Life Sciences

2 The image adapted for the cover was Highly Commended in the Wellcome Trust/BBC HOW IS SCIENCE CHANGING US? Imagine Photography Competition 2005 and is used by permission of the photographer, Ivan Burn.

3 Physics of the Life Sciences Jay Newman 1 23

4 Jay Newman Union College Department of Physics and Astronomy Schenectady, NY 12308, USA ISBN: e-isbn: DOI: / Library of Congress Control Number: Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper springer.com

5 About the Author Jay Newman is the R. Gordon Gould Professor of Physics at Union College where he has taught for 30 years. While studying for his PhD in physics at New York University, he developed a keen interest in biophysics and did a three-year postdoctoral fellowship in the Biophysics Department of Johns Hopkins University. Since joining the faculty at Union College, Professor Newman has taught and developed more than 15 different courses, led student terms abroad in science research in Italy, and also spent a year at Stanford University. The experiences abroad with students stemmed from his previous stays as a Visiting Professor in Italy, once in Pavia and six times in Palermo. His research has been on the structure, dynamics and interactions of biomolecules using laser light scattering and other physical methods. He has 60 publications, many co-authored with some of the 30 plus undergraduate students who have done research projects in his laboratory, and has received two grants from the Research Corporation and five multiyear grants from the National Science Foundation for both research and teaching. About 15 years ago, he developed a special introductory physics course for life science students at Union College, which was the basis for this text. The idea behind the course and this book is to show the essential connections between physics and modern life sciences. Motivating this new approach to an introductory course was Professor Newman s firm belief, developed over his early training and now reinforced by almost daily news reports, that modern biology and medicine are becoming ever more quantitative and dependent on an understanding of physics fundamentals, methodology, technology, and modes of thinking. Building this bridge is the purpose and goal of Physics of the Life Sciences. A BOUT THE AUTHOR V

6 Preface This textbook has its origins in a course that I began developing at Union College in the mid-1980s to teach physics to life science students in a way that would interest them and show the connections of fundamental physics to modern biology and medicine. From my own research experiences and interests in biophysics, I know that almost all areas of modern life sciences integrally involve physics in both experimental techniques and in basic understanding of process or function. However, I and many colleagues with whom I have spoken have been unhappy over the years with published attempts to direct a textbook to this audience. Most such texts are watered down engineering physics books with occasional added sections on related biology topics that are easy to skip over or assign students to read on their own. As I set out to write this textbook, I had certain definite goals in mind. I wanted to write a book that was truly directed at life science students, one that integrated modern biology, biophysics, and medical techniques into the presentation of the material. Believing in the less is more credo, I chose to omit certain standard topics that are usually included in texts for this audience, while expanding on topics that have more relevance to the life and biomedical sciences. From my experience teaching to these students, I also wanted a book that would be shorter and could be fully covered in a two-semester course. Although students at Union College and comparable institutions taking this introductory course have all had some calculus, only algebra and trigonometry are used in the main body of the text. At this level, I believe that calculus adds little to the understanding of the material and can detract from focusing on the basic physical ideas. However, I have sprinkled in optional boxed calculations that do use some calculus where I felt they truly added to the discussion (averaging less than one box per chapter). These sidebars can be omitted without any loss of continuity. The order of topics for this text follows a more or less traditional sequence. An exception to this is the presentation of one-dimensional mechanics through forces and energy before introducing vectors and generalizing to motion in more than one dimension. This allows students to focus on the physics concepts of kinematics, forces, and energy without being distracted by the ideas of vector analysis. Beyond the order of topics, the presentation of material is unique in that, wherever possible, themes from biology or medicine are used to present the physics material. The material speaks to life science students. Rather than optional sections at the end of occasional chapters, life science themes are plentiful and integral to the text. The role of these topics here is more fundamental, as can be gleaned from a list of some examples. The early introduction of diffusion as an example of motion (full section in Chapter 2). The early introduction of motion in a viscous fluid as an example of one-dimensional motion, development of Hooke s law and elasticity with applications to biomaterials and viscoelasticity, protein structure, and molecular dynamics calculations (all in Chapter 3). Discussion of centrifugation in Chapter 5. P REFACE VII

7 Examples of rotational motion kinematics of a bacteria and of a rotary motor protein, the atomic force microscope, rotational diffusion, and cell membrane dynamics (all in Chapter 7). A chapter (9) on viscous fluids with discussions of blood, other complex fluids, the human circulatory system, surface tension, and capillarity. A chapter (11) on sound with extensive discussions on the ear and on ultrasound. A chapter (13) with a molecular discussion of entropy, a section on Gibbs free energy, a section on biological applications of statistical thermodynamics, and a section on biological applications of nonlinear dynamics. Chapters (14 15) on electric forces, fields, and energy with sections on electrophoresis, macromolecular charges in solution, modern electrophoresis methods, electrostatic applications to native and synthetic macromolecules, an introduction to capacitors entirely through a discussion of cell membranes, and sections on membrane channels and electric potential mapping of the human body: heart, muscle, and brain. A chapter (16) on electric current and cell membranes covering circuits through membrane models: included are sections on membrane electrical currents, an overview of nerve structure and function including measurement techniques such as patch-clamping, the electrical properties of neurons, and a second section on membrane channels with a discussion of single-channel recording. Chapters on electromagnetic induction and waves (18 19) that include discussion of MEG (magnetoencephalography) using SQUIDs, an entire section on NMR, and sections on magnetic resonance imaging, laser tweezers, the quantum theory of radiation concepts (revisited later), and the interaction of radiation with matter, the last a primer on spectroscopy, including absorption spectroscopy, scattering, and fluorescence. Four chapters (20 23) on optics include a section on optical fibers and their applications in medicine, a section on the human eye, sections on the new light microscopies (dark field, fluorescence, phase contrast, DIC, confocal and multiphoton methods), discussion of polarization in biology, including birefringence and dichroism techniques, and sections on the transmission electron microscope, scanning EM and scanning transmission EM, and x-rays and computed tomography (CT) methods. Three chapters (24 26) on modern physics (many of these ideas have been introduced and used throughout the book) include discussions of the scanning tunneling microscope, a section on the laser and its applications in biology and medicine, including holography. The chapter on nuclear physics and medical applications (26) includes sections on dosimetry and biological effects of radiation, radioisotopes, and nuclear medicine, and the medical imaging methods SPECT (single photon emission computer tomography) and PET (positron emission tomography). As mentioned above, we ve chosen to omit some standard topics that are either not central to the life science themes or that students find very opaque. Omitted are such topics as Kepler s laws, heat engines, induction and LR/LRC circuits, AC circuits, special relativity kinematics, particle physics, and astrophysics; Gauss s law and Ampere s law are presented in optional sections at the end of appropriate chapters. Each chapter contains three types of learning aides for the student: open-ended questions, multiple-choice questions, and quantitative problems. In about 60 of these per chapter, we have tried to include a wide selection related to the life sciences. Complete solutions to all of the multiple choice and other problems are available to instructors. There are also a number of worked examples in the chapters, averaging over six per chapter, and about 900 photos and line drawings to illustrate concepts in the text, with many in full color. Jay Newman Schenectady, NY VIII P REFACE

8 Acknowledgments First I d like to thank the American Institute of Physics Press and both Maria Taylor and Elias Greenbaum for suggesting this project and providing a grant that gave me most of a year free from teaching to start writing this textbook. I ve benefited greatly from collaborations with three colleagues on its development. David Peak, a former Union College colleague now at Utah State, edited portions of the manuscript and made many suggestions on the presentation of the material. Larry Brehm, formerly at IBM and now at SUNY Potsdam, contributed to the end-of-chapter problems for a number of the chapters, particularly in the mechanics and optics portions. Scott LaBrake, at Union College, checked and solved all the problems in the book, and wrote the solutions manual, as well as taught from preliminary editions of the book. Thanks also to the many students who learned their introductory physics from preliminary versions of this text and put up with typographical errors and occasional unsolvable problems. Some of these students worked through essentially all the problems in the book helping to find errors as well. I also thank my colleagues at Union College for their interest and support in this project and for numerous discussions about physics pedagogy. The staff at Springer, including David Packer, Anushka Hosain, and all the production team, has been most helpful in seeing this project to fruition. Finally, I thank my extended family for their support, encouragement, and love over these many years, especially my wife, Maia. A CKNOWLEDGMENTS IX

9 Contents Preface vii Acknowledgments ix List of Tables xvii 1 Introduction Science, Physics, and Biology Plan of This Book Two Examples of Biophysical Systems: The Single Cell E. coli Bacteria and the Human Heart The Atomic Nature of Matter Mass, Density, and the Size of Atoms: Exercises in Estimation and Units. 8 Chapter Summary Questions/Problems Newton s Laws of Motion for a Particle Moving in One Dimension Position, Velocity, and Acceleration in One Dimension Newton s First Law of Motion Force in One Dimension Mass and Newton s Law of Gravity Newton s Second Law of Motion in One Dimension Newton s Third Law Diffusion Chapter Summary Questions/Problems Applications of Newton s Laws of Motion in One Dimension The Constant Force Motion in a Viscous Fluid Hooke s Law and Oscillations Forces on Solids and Their Elastic Response; Biomaterials and Viscoelasticity Structure and Molecular Dynamics of Proteins Chapter Summary Questions/Problems Work and Energy in One Dimension Work Kinetic Energy and the Work Energy Theorem Potential Energy and the Conservation of Energy Forces from Energy Power C ONTENTS XI

10 Chapter Summary Questions/Problems Motion, Forces, and Energy in More than One Dimension Vector Algebra Kinematics Dynamics Work and Energy Contact Frictional Forces Circular Motion Dynamics Centrifugation Chapter Summary Questions/Problems Momentum Momentum Center of Mass Center of Mass Motion: Newton s Second Law and Conservation of Momentum Chapter Summary Questions/Problems Rotational Motion Rotational Kinematics Rotational Energy Torque and Rotational Dynamics of a Rigid Body Angular Momentum Atomic Force Microscopy Rotational Diffusion; Cell Membrane Dynamics Static Equilibrium Chapter Summary Questions/Problems Ideal Fluids Introduction Pressure Dynamics of Nonviscous Fluids: Types of Flow Conservation Laws of Fluid Dynamics Hydrostatics: Effects of Gravity The Measurement of Pressure Chapter Summary Questions/Problems Viscous Fluids Viscosity of Simple Fluids Blood and Other Complex Fluids The Human Circulatory System Surface Tension and Capillarity Chapter Summary Questions/Problems Waves and Resonance Simple Harmonic Motion Revisited: Damping and Resonance Wave Concepts XII C ONTENTS

11 3. Traveling Waves Waves at a Boundary: Interference Standing Waves and Resonance Chapter Summary Questions/Problems Sound Basics Intensity of Sound Superposition of Sound Waves Producing Sound The Human Ear: Physiology and Function The Doppler Effect in Sound Ultrasound Chapter Summary Questions/Problems Temperature and Heat Temperature and Thermal Equilibrium Thermal Expansion and Stress Internal Energy and the Ideal Gas The First Law of Thermodynamics Thermal Properties of Matter Vapor and Osmotic Pressure; Membrane Transport and the Kidney Heat Transfer Mechanisms Chapter Summary Questions/Problems Thermodynamics: Beyond the First Law Entropy and the Second Law of Thermodynamics Gibbs Free Energy Biological Applications of Statistical Thermodynamics Chapter Summary Questions/Problems Electric Forces and Fields Electric Charge and Charge Conservation Coulomb s Law Conductors and Insulators Electric Fields Principles of Electrophoresis; Macromolecular Charges in Solution Modern Electrophoresis Methods (Optional) Gauss s Law Chapter Summary Questions/Problems Electric Energy and Potential Electric Potential Energy Electric Potential Electric Dipoles and Charge Distributions Atomic and Molecular Electrical Interactions Static Electrical Properties of Bulk Matter Capacitors and Membranes C ONTENTS XIII

12 7. Membrane Channels: Part I Electric Potential Mapping of the Human Body: Heart, Muscle, and Brain Chapter Summary Questions/Problems Electric Current and Cell Membranes Electric Current and Resistance Ohm s Law and Electrical Measurements Membrane Electrical Currents Overview of Nerve Structure and Function; Measurement Techniques Electrical Properties of Neurons Membrane Channels: Part II Chapter Summary Questions/Problems Magnetic Fields Magnetic Fields and Forces Torque and Force on a Magnetic Dipole The Stern Gerlach Experiment and Electron Spin Producing B fields (Optional) Ampere s Law Chapter Summary Questions/Problems Electromagnetic Induction and Radiation Electromagnetic Induction and Faraday s Law Nuclear Magnetic Resonance (NMR) Magnetic Resonance Imaging Maxwell s Equations; Electromagnetic Radiation Chapter Summary Questions/Problems Electromagnetic Waves Electromagnetic Waves Laser Tweezers Polarization The Electromagnetic Spectrum The Quantum Theory of Radiation: Concepts The Interaction of Radiation with Matter; A Primer on Spectroscopy. 491 Chapter Summary Questions/Problems Geometrical Optics Optical Properties of Matter Light at an Interface Spherical Mirrors Optical Fibers and Their Applications in Medicine Chapter Summary Questions/Problems Optical Lenses and Devices Optical Lenses The Human Eye Optical Devices: The Magnifying Glass and Optical Microscope XIV C ONTENTS

13 Chapter Summary Questions/Problems Wave Optics Diffraction and Interference of Light Single-, Double-, and Multiple-Slits and Interferometers Resolution Chapter Summary Questions/Problems Imaging Using Wave Optics The New Light Microscopies Optical Activity; Applications of Light Polarization Electron Microscopy X-rays: Diffraction and Computed Tomography (CT) Chapter Summary Questions/Problems Special Relativity and Quantum Physics Special Relativity: Mass Energy and Dynamics Overview of Quantum Theory Wave Functions; the Schrödinger Equation Uncertainty Principle; Scanning Tunneling Microscope Chapter Summary Questions/Problems The Structure of Matter The Simple Hydrogen Atom Quantum Numbers and Spin The Pauli Exclusion Principle; The Periodic Table and Chemistry Spectroscopy of Biomolecules Revisited Lasers and Their Applications in Biology and Medicine Chapter Summary Questions/Problems Nuclear Physics and Medical Applications Nuclear Size, Structure, and Forces Binding Energy and Nuclear Stability Types of Radiation and Their Measurement Half-Life and Radioactive Dating Dosimetry and Biological Effects of Radiation Radioisotopes and Nuclear Medicine SPECT and PET: Radiation Tomography Fission and Fusion Chapter Summary Questions/Problems Appendix I Review of Mathematics Appendix II Table of the Elements Appendix III Answers to Odd-Numbered Multiple Choice and Problems Figure Credits Index C ONTENTS XV

14 List of Tables 1.1 SI Units of Measure Commonly Used Prefixes Mass Densities Units of Distance Table of Position Versus Time One-Dimensional Kinematic Relations Typical Reynolds Numbers Terminal Velocities of Various Objects Data for Hanging Mass on a Spring Steps in Vector Addition Coefficients of Friction Typical Sedimentation Coefficients Distances and Masses of Portions of the Typical Human Body Moments of Inertia of Various Symmetric Objects Kinematic and Dynamic Equations for Rotational-Translational Motion Method to Solve Static Equilibrium Problems Densities of Some Substances Viscosities of Water and Blood Densities and Velocities of Sound Intensities of Sounds Acoustic Impedances Comparison of Temperatures in Different Units Coefficients of Expansion Specific Heats Latent Heats Average Bond Dissociation Energies Metabolic Activity Rates Thermal Conductivities Spontaneity of Thermodynamic Processes Electric Fields of Various Geometries Screening Lengths at Different Ionic Strengths of Solution Dielectric Constants Resistivities Typical Cellular Ion Concentrations and Nernst Potentials Weak Magnetic Fields Water Content of Normal Human Tissue Types of Atomic or Molecular Transitions Produced by EM Radiation Refractive Indices Sign Convention for Mirror Equation Sign Convention for Thin Lenses CT Numbers Some Ground State Electron Configurations Half-Lives of Some Radioactive Nuclides Relative Biological Effectiveness of Radiation Typical Human Radiation Doses Commonly Used Radioisotopes in Medicine L IST OF TABLES XVII