Physics of the Life Sciences

Physics of the Life Sciences

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.

Physics of the Life Sciences Jay Newman 1 23

Jay Newman Union College Department of Physics and Astronomy Schenectady, NY 12308, USA ISBN: 978-0-387-77258-5 e-isbn: 978-0-387-77259-2 DOI: 10.1007/978-0-387-77259-2 Library of Congress Control Number: 2008929543 2008 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 987654321 springer.com

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

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

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

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

Contents Preface.......................................................... vii Acknowledgments.................................................. ix List of Tables.................................................... xvii 1 Introduction.................................................. 1 1. Science, Physics, and Biology.................................. 1 2. Plan of This Book............................................ 3 3. Two Examples of Biophysical Systems: The Single Cell E. coli Bacteria and the Human Heart........................ 4 4. The Atomic Nature of Matter................................... 6 5. Mass, Density, and the Size of Atoms: Exercises in Estimation and Units. 8 Chapter Summary........................................... 12 Questions/Problems.......................................... 13 2 Newton s Laws of Motion for a Particle Moving in One Dimension... 15 1. Position, Velocity, and Acceleration in One Dimension............. 16 2. Newton s First Law of Motion................................. 21 3. Force in One Dimension...................................... 23 4. Mass and Newton s Law of Gravity............................. 25 6. Newton s Second Law of Motion in One Dimension................ 28 7. Newton s Third Law......................................... 30 8. Diffusion.................................................. 33 Chapter Summary........................................... 35 Questions/Problems.......................................... 36 3 Applications of Newton s Laws of Motion in One Dimension......... 43 1. The Constant Force.......................................... 43 2. Motion in a Viscous Fluid..................................... 49 3. Hooke s Law and Oscillations................................. 53 4. Forces on Solids and Their Elastic Response; Biomaterials and Viscoelasticity.......................................... 60 5. Structure and Molecular Dynamics of Proteins.................... 66 Chapter Summary........................................... 71 Questions/Problems.......................................... 71 4 Work and Energy in One Dimension............................. 77 1. Work..................................................... 77 2. Kinetic Energy and the Work Energy Theorem.................... 80 3. Potential Energy and the Conservation of Energy.................. 82 4. Forces from Energy.......................................... 87 5. Power..................................................... 91 C ONTENTS XI

Chapter Summary........................................... 92 Questions/Problems.......................................... 93 5 Motion, Forces, and Energy in More than One Dimension........... 97 1. Vector Algebra............................................. 97 2. Kinematics................................................ 101 3. Dynamics................................................. 106 4. Work and Energy........................................... 110 5. Contact Frictional Forces.................................... 113 6. Circular Motion Dynamics................................... 118 7. Centrifugation............................................. 122 Chapter Summary.......................................... 124 Questions/Problems......................................... 125 6 Momentum................................................. 139 1. Momentum............................................... 139 2. Center of Mass............................................ 145 3. Center of Mass Motion: Newton s Second Law and Conservation of Momentum.............................. 150 Chapter Summary.......................................... 155 Questions/Problems......................................... 156 7 Rotational Motion........................................... 161 1. Rotational Kinematics....................................... 162 2. Rotational Energy.......................................... 165 3. Torque and Rotational Dynamics of a Rigid Body................. 172 4. Angular Momentum........................................ 179 5. Atomic Force Microscopy................................... 185 6. Rotational Diffusion; Cell Membrane Dynamics.................. 186 7. Static Equilibrium.......................................... 189 Chapter Summary.......................................... 193 Questions/Problems......................................... 194 8 Ideal Fluids................................................. 205 1. Introduction............................................... 205 2. Pressure.................................................. 207 3. Dynamics of Nonviscous Fluids: Types of Flow.................. 209 4. Conservation Laws of Fluid Dynamics.......................... 211 5. Hydrostatics: Effects of Gravity............................... 217 6. The Measurement of Pressure................................. 222 Chapter Summary.......................................... 225 Questions/Problems......................................... 225 9 Viscous Fluids............................................... 231 1. Viscosity of Simple Fluids................................... 231 2. Blood and Other Complex Fluids.............................. 236 3. The Human Circulatory System............................... 237 4. Surface Tension and Capillarity............................... 241 Chapter Summary.......................................... 244 Questions/Problems......................................... 245 10 Waves and Resonance........................................ 249 1. Simple Harmonic Motion Revisited: Damping and Resonance....... 249 2. Wave Concepts............................................ 254 XII C ONTENTS

3. Traveling Waves........................................... 256 4. Waves at a Boundary: Interference............................. 258 5. Standing Waves and Resonance............................... 261 Chapter Summary.......................................... 264 Questions/Problems......................................... 265 11 Sound...................................................... 269 1. Basics................................................... 269 2. Intensity of Sound.......................................... 271 3. Superposition of Sound Waves................................ 273 4. Producing Sound........................................... 279 5. The Human Ear: Physiology and Function....................... 282 6. The Doppler Effect in Sound................................. 286 7. Ultrasound................................................ 288 Chapter Summary.......................................... 292 Questions/Problems......................................... 292 12 Temperature and Heat........................................ 297 1. Temperature and Thermal Equilibrium.......................... 297 2. Thermal Expansion and Stress................................ 300 3. Internal Energy and the Ideal Gas............................. 304 4. The First Law of Thermodynamics............................ 308 5. Thermal Properties of Matter................................. 312 6. Vapor and Osmotic Pressure; Membrane Transport and the Kidney............................................ 317 7. Heat Transfer Mechanisms................................... 321 Chapter Summary.......................................... 325 Questions/Problems......................................... 326 13 Thermodynamics: Beyond the First Law........................ 331 1. Entropy and the Second Law of Thermodynamics................. 331 2. Gibbs Free Energy......................................... 337 3. Biological Applications of Statistical Thermodynamics............ 341 Chapter Summary.......................................... 344 Questions/Problems......................................... 345 14 Electric Forces and Fields..................................... 347 1. Electric Charge and Charge Conservation....................... 347 2. Coulomb s Law............................................ 349 3. Conductors and Insulators.................................... 352 4. Electric Fields............................................. 353 5. Principles of Electrophoresis; Macromolecular Charges in Solution... 360 6. Modern Electrophoresis Methods.............................. 361 7. (Optional) Gauss s Law..................................... 363 Chapter Summary.......................................... 366 Questions/Problems......................................... 367 15 Electric Energy and Potential.................................. 373 1. Electric Potential Energy.................................... 373 2. Electric Potential........................................... 375 3. Electric Dipoles and Charge Distributions....................... 378 4. Atomic and Molecular Electrical Interactions.................... 382 5. Static Electrical Properties of Bulk Matter....................... 384 6. Capacitors and Membranes................................... 386 C ONTENTS XIII

7. Membrane Channels: Part I.................................. 392 8. Electric Potential Mapping of the Human Body: Heart, Muscle, and Brain..................................... 393 Chapter Summary.......................................... 396 Questions/Problems......................................... 397 16 Electric Current and Cell Membranes.......................... 401 1. Electric Current and Resistance............................... 401 2. Ohm s Law and Electrical Measurements....................... 406 3. Membrane Electrical Currents................................ 412 4. Overview of Nerve Structure and Function; Measurement Techniques. 415 5. Electrical Properties of Neurons............................... 418 6. Membrane Channels: Part II.................................. 421 Chapter Summary.......................................... 424 Questions/Problems......................................... 425 17 Magnetic Fields............................................. 431 1. Magnetic Fields and Forces.................................. 432 2. Torque and Force on a Magnetic Dipole........................ 437 3. The Stern Gerlach Experiment and Electron Spin................. 438 4. Producing B fields.......................................... 439 5. (Optional) Ampere s Law................................... 444 Chapter Summary.......................................... 446 Questions/Problems......................................... 446 18 Electromagnetic Induction and Radiation....................... 453 1. Electromagnetic Induction and Faraday s Law.................... 453 2. Nuclear Magnetic Resonance (NMR)........................... 460 3. Magnetic Resonance Imaging................................. 467 4. Maxwell s Equations; Electromagnetic Radiation................. 470 Chapter Summary.......................................... 472 Questions/Problems......................................... 472 19 Electromagnetic Waves....................................... 477 1. Electromagnetic Waves...................................... 477 2. Laser Tweezers............................................ 482 3. Polarization............................................... 485 4. The Electromagnetic Spectrum................................ 488 5. The Quantum Theory of Radiation: Concepts.................... 489 6. The Interaction of Radiation with Matter; A Primer on Spectroscopy. 491 Chapter Summary.......................................... 497 Questions/Problems......................................... 498 20 Geometrical Optics.......................................... 503 1. Optical Properties of Matter.................................. 503 2. Light at an Interface........................................ 505 3. Spherical Mirrors.......................................... 509 4. Optical Fibers and Their Applications in Medicine................ 514 Chapter Summary.......................................... 517 Questions/Problems......................................... 518 21 Optical Lenses and Devices.................................... 523 1. Optical Lenses............................................. 523 2. The Human Eye........................................... 530 3. Optical Devices: The Magnifying Glass and Optical Microscope..... 536 XIV C ONTENTS

Chapter Summary.......................................... 538 Questions/Problems......................................... 538 22 Wave Optics................................................ 543 1. Diffraction and Interference of Light........................... 543 2. Single-, Double-, and Multiple-Slits and Interferometers........... 548 3. Resolution................................................ 556 Chapter Summary.......................................... 559 Questions/Problems......................................... 560 23 Imaging Using Wave Optics................................... 563 1. The New Light Microscopies................................. 563 2. Optical Activity; Applications of Light Polarization............... 568 3. Electron Microscopy........................................ 571 4. X-rays: Diffraction and Computed Tomography (CT).............. 573 Chapter Summary.......................................... 577 Questions/Problems......................................... 578 24 Special Relativity and Quantum Physics......................... 581 1. Special Relativity: Mass Energy and Dynamics.................. 581 2. Overview of Quantum Theory................................ 585 3. Wave Functions; the Schrödinger Equation...................... 590 4. Uncertainty Principle; Scanning Tunneling Microscope............ 593 Chapter Summary.......................................... 598 Questions/Problems......................................... 600 25 The Structure of Matter...................................... 603 1. The Simple Hydrogen Atom.................................. 603 2. Quantum Numbers and Spin.................................. 607 3. The Pauli Exclusion Principle; The Periodic Table and Chemistry.... 610 4. Spectroscopy of Biomolecules Revisited........................ 613 5. Lasers and Their Applications in Biology and Medicine............ 618 Chapter Summary.......................................... 627 Questions/Problems......................................... 628 26 Nuclear Physics and Medical Applications....................... 633 1. Nuclear Size, Structure, and Forces............................ 633 2. Binding Energy and Nuclear Stability.......................... 635 3. Types of Radiation and Their Measurement...................... 638 4. Half-Life and Radioactive Dating.............................. 642 5. Dosimetry and Biological Effects of Radiation................... 645 6. Radioisotopes and Nuclear Medicine........................... 647 7. SPECT and PET: Radiation Tomography........................ 649 8. Fission and Fusion......................................... 652 Chapter Summary.......................................... 655 Questions/Problems......................................... 656 Appendix I Review of Mathematics........................... 659 Appendix II Table of the Elements............................ 665 Appendix III Answers to Odd-Numbered Multiple Choice and Problems............................................. 669 Figure Credits.............................................. 687 Index................................................... 691 C ONTENTS XV

List of Tables 1.1 SI Units of Measure............................................ 9 1.2 Commonly Used Prefixes........................................ 9 1.3 Mass Densities............................................... 10 2.1 Units of Distance............................................. 17 2.2 Table of Position Versus Time................................... 17 3.1 One-Dimensional Kinematic Relations............................ 45 3.2 Typical Reynolds Numbers...................................... 50 3.3 Terminal Velocities of Various Objects............................ 53 3.4 Data for Hanging Mass on a Spring............................... 54 5.1 Steps in Vector Addition....................................... 101 5.2 Coefficients of Friction........................................ 116 5.3 Typical Sedimentation Coefficients.............................. 123 6.1 Distances and Masses of Portions of the Typical Human Body........ 157 7.1 Moments of Inertia of Various Symmetric Objects.................. 168 7.2 Kinematic and Dynamic Equations for Rotational-Translational Motion... 181 7.3 Method to Solve Static Equilibrium Problems...................... 191 8.1 Densities of Some Substances.................................. 206 9.1 Viscosities of Water and Blood................................. 232 11.1 Densities and Velocities of Sound............................... 271 11.2 Intensities of Sounds.......................................... 273 11.3 Acoustic Impedances......................................... 289 12.1 Comparison of Temperatures in Different Units.................... 299 12.2 Coefficients of Expansion...................................... 301 12.3 Specific Heats............................................... 312 12.4 Latent Heats................................................ 314 12.5 Average Bond Dissociation Energies............................. 316 12.6 Metabolic Activity Rates...................................... 321 12.7 Thermal Conductivities........................................ 323 13.1 Spontaneity of Thermodynamic Processes......................... 338 14.1 Electric Fields of Various Geometries............................ 357 14.2 Screening Lengths at Different Ionic Strengths of Solution........... 361 15.1 Dielectric Constants.......................................... 385 16.1 Resistivities................................................. 404 16.2 Typical Cellular Ion Concentrations and Nernst Potentials............ 415 18.1 Weak Magnetic Fields........................................ 459 18.2 Water Content of Normal Human Tissue.......................... 468 19.1 Types of Atomic or Molecular Transitions Produced by EM Radiation.... 492 20.1 Refractive Indices............................................ 504 20.2 Sign Convention for Mirror Equation............................ 513 21.1 Sign Convention for Thin Lenses................................ 525 23.1 CT Numbers................................................ 576 25.1 Some Ground State Electron Configurations....................... 612 26.1 Half-Lives of Some Radioactive Nuclides......................... 643 26.2 Relative Biological Effectiveness of Radiation..................... 646 26.3 Typical Human Radiation Doses................................ 646 26.4 Commonly Used Radioisotopes in Medicine....................... 648 L IST OF TABLES XVII