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Table of Contents
Preface #8,0,-32767Acknowledgments #12,0,-32767Part I Fundamentals #14,0,-32767 1 Introduction #16,0,-32767 2 Planning and Carrying Out Experiments #20,0,-32767 2.1 Literature Research #20,0,-32767 2.2 Reading Scientific Papers #21,0,-32767 2.3 Experimental Design #22,0,-32767 2.4 Modeling #24,0,-32767 2.5 Important Guidelines for Conducting Experiments #26,0,-32767 Preparation #26,0,-32767 Safety #26,0,-32767 Pilot Testing #26,0,-32767 Taking Data #26,0,-32767 2.6 Lab Notebooks #26,0,-32767 2.7 Troubleshooting #27,0,-32767 3 Presenting Your Results #32,0,-32767 3.1 The Process of Scientific Communication #32,0,-32767 3.2 Data Visualization #33,0,-32767 Graphs #33,0,-32767 Images #35,0,-32767 Diagrams #35,0,-32767 3.3 Writing Scientific Papers #36,0,-32767 3.4 Preparing, Delivering, and Listening to Talks #39,0,-32767 Listening to Talks #39,0,-32767 3.5 Preparing and Presenting Posters #40,0,-32767 4 Uncertainty and Statistics #42,0,-32767 4.1 Random vs. Systematic Errors #43,0,-32767 Accuracy vs. Precision #43,0,-32767 Where Do These Systematic Errors Come From? #44,0,-32767 4.2 Methods of Determining Uncertainty #45,0,-32767 Instrumental Uncertainty #45,0,-32767 Multiple Trials #45,0,-32767 4.3 Standard Error of the Mean and Probability Distributions #45,0,-32767 4.3.1 Sample vs Population and the Gaussian Distribution #45,0,-32767 4.3.2 Standard Deviation vs. Standard Error of the Mean #47,0,-32767 4.3.3 Other Distributions #47,0,-32767 4.3.4 Median and Mode #47,0,-32767 4.4 Confidence Intervals #48,0,-32767 4.5 Student’s t-Distribution #49,0,-32767 4.6 Significant Figures #51,0,-32767 4.7 Quantitative Comparisons, or How Not to Be Misled by Error Bars #51,0,-32767 4.8 Propagating Errors #52,0,-32767 Direct Substitution #52,0,-32767 Linear Approximation #53,0,-32767 Multiple Error Contributions #53,0,-32767 Addition in Quadrature #53,0,-32767 4.9 More of the Instrumental Uncertainty Method, Including “Absolute Tolerance” #54,0,-32767 4.10 Parameter Fitting #56,0,-32767 4.11 Measurement Errors and χ2 (also known as chi square) #60,0,-32767 Interpreting χ2 #60,0,-32767 Fitting Routines and How to Make Them Work for You #61,0,-32767 Outliers and Outlier Rejection #62,0,-32767 4.12 What to Do When Something Goes Wrong #63,0,-32767 4.13 Homework Problems #64,0,-32767 Acknowledgment #65,0,-32767 5 Scientific Ethics #66,0,-32767 5.1 A Brief Overview of Scientific Ethics #67,0,-32767 5.2 FFP: The Cardinal Sins #67,0,-32767 5.3 Data Ethics #69,0,-32767 5.4 Publishing and Credit #71,0,-32767 5.5 Academia #73,0,-32767 5.6 Equality and Equity #75,0,-32767 5.7 Financial Considerations #76,0,-32767 5.8 Safety #78,0,-32767 5.9 Communication #79,0,-32767 5.10 Regulations #81,0,-32767 5.11 Choice of Research #82,0,-32767Part II Tools of an Experimentalist #84,0,-32767 6 Analog Electronics #86,0,-32767 6.1 Introduction #87,0,-32767 6.2 Input and Output Impedance: Part 1 #87,0,-32767 Motivation, Voltage Dividers #87,0,-32767 Introduction #88,0,-32767 What Is an Ideal Battery? #88,0,-32767 Ground vs. Common, Behavior of Real Batteries with “No Load” vs. with Rload #89,0,-32767 Definition of Output Impedance #90,0,-32767 How to Measure Output Impedance #90,0,-32767 Generalization of Output Impedance, Perfect Buffers #91,0,-32767 Functional Blocks, the Scientific Debugging Process #91,0,-32767 Input Impedance #92,0,-32767 An Example of Complex Input Impedance #92,0,-32767 Combining the Ideas of Input and Output Impedance: Loading Effects #93,0,-32767 How to Measure Input Impedance #94,0,-32767 6.3 Input and Output Impedance: Part 2 #95,0,-32767 How to Calculate Input Impedance by Looking at a Schematic Diagram #95,0,-32767 How to Calculate Output Impedance by Looking at a Schematic Diagram #96,0,-32767 Back to Our Motivational Example #97,0,-32767 Other Examples, Application to Debugging #97,0,-32767 Input and Output Impedance of Filters #98,0,-32767 6.4 Amplifier Fundamentals #99,0,-32767 6.5 Capacitively Coupled Interference #101,0,-32767 6.6 Common vs. Ground, Inductively Coupled Interference, and Ground Loops #102,0,-32767 Common vs. Ground #102,0,-32767 Single-Ended vs. Differential Amplifiers #103,0,-32767 Inductively Coupled Interference #104,0,-32767 Background #104,0,-32767 Interference in a Circuit #106,0,-32767 How to Minimize It #106,0,-32767 Ground Loops #107,0,-32767 6.7 Noise #109,0,-32767 Noise Amplitude #110,0,-32767 Combining Noise Sources #112,0,-32767 Fourier Spectral Characteristics of Noise #113,0,-32767 6.8 Negative Feedback and Op Amps #117,0,-32767 6.9 Bode Plots and Oscillations from the Feedback Loop #117,0,-32767 6.10 Simulation of Analog Circuits #117,0,-32767 Lab 6A Input and Output Impedance Revisited, Surprising Effects of Capacitance #117,0,-32767 Introduction #118,0,-32767 Lab 6B Intermediate-level Scope Mastery #120,0,-32767 Introduction #121,0,-32767 Lab 6C Introduction to Amplifiers, Capacitively Coupled Interference, and Feedback Oscillations #123,0,-32767 Introduction #123,0,-32767 Lab 6D Inductively Coupled Interference and Ground Loops #127,0,-32767 Lab 6E Amplifier Noise and Introduction to LabVIEW #132,0,-32767 Part 1: DC Offsets and Amplifier Noise #132,0,-32767 Part 2: Introduction to LabVIEW #134,0,-32767 Lab 6F Lock-In Amplifiers #137,0,-32767 Introduction and Background #137,0,-32767 Experimental Procedure #143,0,-32767 Lab 6G Introduction to Op Amps #145,0,-32767 Lab 6H More on Op Amps #145,0,-32767 6.11 Homework Problems #145,0,-32767 7 Fundamentals of Interfacing Experiments with Computers #146,0,-32767 7.1 Introduction: The Difference between Digital and Analog #146,0,-32767 Approaches to Interfacing #147,0,-32767 7.2 Sampling Rate, Resolution, and the Importance of Analog Amplification #148,0,-32767 7.3 The Nyquist Frequency, Aliasing, Windowing, and Experimental Fourier Analysis #149,0,-32767 Aliasing #152,0,-32767 Windowing #153,0,-32767 7.4 Preview of the Arduino #155,0,-32767 8 Digital Electronics #156,0,-32767 8.1 Introduction #157,0,-32767 8.2 Truth Tables #157,0,-32767 8.3 Gates #158,0,-32767 8.3.1 Basic Gates #158,0,-32767 8.3.2 Multi-Gate Circuits #160,0,-32767 8.3.3 CMOS Logic Gates #161,0,-32767 8.4 Boolean Algebra #161,0,-32767 8.4.1 Variables #162,0,-32767 8.4.2 Operators #162,0,-32767 8.4.3 Expressions #162,0,-32767 8.4.4 Algebraic Relations #162,0,-32767 8.5 Logic Design #164,0,-32767 8.5.1 Sum-of-Products #164,0,-32767 8.5.2 Product-of-Sums #165,0,-32767 8.6 Common Logic Functions #166,0,-32767 8.6.1 Coders/Decoders #166,0,-32767 8.7 Arithmetic Logic #168,0,-32767 8.7.1 Half-Adder #168,0,-32767 8.7.2 The Full-Adder #168,0,-32767 8.8 Sequential Logic #169,0,-32767 8.8.1 The Flip-Flop #169,0,-32767 8.8.2 Switch De-Bouncing with the  Flip-Flop #170,0,-32767 8.8.3 Simple Counters #172,0,-32767 8.9 Synchronous Logic #173,0,-32767 8.9.1 Describing Synchronous Systems #174,0,-32767 8.9.2 Designing Synchronous Circuits with D-Type Flip-Flops #175,0,-32767 8.9.3 Excluded States in Synchronous Logic #176,0,-32767 8.9.4 External Inputs #176,0,-32767 8.9.5 Resetting Synchronous Circuits #177,0,-32767 8.10 Introduction to Verilog #178,0,-32767 Lab 8A Digital Logic #178,0,-32767 8A.1 Combinatorial Logic #178,0,-32767 8A.2 Sequential Logic #180,0,-32767 8A.3 Synchronous Sequential Machines #182,0,-32767 Lab 8B Controlling the World with Arduino #183,0,-32767 Lab 8C Interfacing an Experiment with Arduino #195,0,-32767 Lab 8D Arduino Motor Control #201,0,-32767 Lab 8E Field Programmable Gate Arrays (FPGAs) #206,0,-32767 9 Data Acquisition and Experiment Control with Python #208,0,-32767 Learning Goals #209,0,-32767 9.1 Overview #209,0,-32767 9.1.1 Automation Technologies #209,0,-32767 9.1.2 What This Chapter Is Really About #211,0,-32767 9.2 Safety Precautions #211,0,-32767 9.2.1 Automation Risks #211,0,-32767 9.3 Python: An Introduction and Primer #212,0,-32767 9.3.1 Programming Best Practices #212,0,-32767 9.3.2 Self-Guided Python Tutorial #214,0,-32767 9.3.3 Working with Python Files #217,0,-32767 9.4 Warm-up Experiment #219,0,-32767 9.4.1 Materials #219,0,-32767 9.4.2 Complete Warm-Up Experiment #220,0,-32767 9.5 Experiment #222,0,-32767 9.5.1 Materials #223,0,-32767 9.5.2 Hardware Limitations #223,0,-32767 9.5.3 Experimental Setup #224,0,-32767 9.5.4 Understanding LabJack Streaming #224,0,-32767 9.5.5 Plan the Software Workflow #224,0,-32767 9.5.6 Create Automation Script #228,0,-32767 9.5.7 Performing Useful Science with Your Experimental System #228,0,-32767 9.6 Advanced Lab: Leverage the PLACE Framework #229,0,-32767 9.7 Homework Problems #237,0,-32767 10 Basic Optics Techniques and Hardware #240,0,-32767 10.1 Laser Safety #241,0,-32767 10.2 Lasers #242,0,-32767 10.3 Optical Hardware #242,0,-32767 Optical Tables and Breadboards #242,0,-32767 Posts, Postholders, and Pedestals #243,0,-32767 10.4 Optical Elements #245,0,-32767 Lenses #246,0,-32767 Mirrors #247,0,-32767 Neutral Density Filters #248,0,-32767 Beamsplitters #248,0,-32767 Polarizers and Waveplates #249,0,-32767 10.5 Beam Expanders #251,0,-32767 10.6 Alignment #251,0,-32767 10.7 Protection, Storage, and Cleaning #253,0,-32767 10.8 Organization #254,0,-32767 Labeling #254,0,-32767 Storage #255,0,-32767 Tools Organization #255,0,-32767 Lab 10A The Quantum Eraser, Simple Version #255,0,-32767 10A.1 Introduction #255,0,-32767 Classical Polarization and Interference #255,0,-32767 Quantum Polarization and Interference #256,0,-32767 10A.2 Precision Optical Alignments #256,0,-32767 Walking the Beam #256,0,-32767 Aligning a Laser with the Grid of Holes #256,0,-32767 10A.3 Mach-Zender Interferometer and the Quantum Eraser #257,0,-32767 Insert Polarizing Beam Splitter Cube and Align the Beam with the Table #257,0,-32767 Insert Mirrors 3 and 4, and Align the Beams #257,0,-32767 Insert NPBS cube and Align the Beams with the Table #258,0,-32767 Adding the Final Polarizer #258,0,-32767 Understanding Interference, and the “Quantum Eraser” #259,0,-32767 11 Laser Beams, Polarization, and Interference #260,0,-32767 11.1 Introduction #260,0,-32767 Learning Goals #260,0,-32767 Additional Reading #261,0,-32767 Pre-Lab Questions #261,0,-32767 11.2 Polarization #261,0,-32767 Lab 11A Polarization and Jones Vectors #265,0,-32767 11A.1 Optical Activity #265,0,-32767 11A.2 Quarter Wave Plates #266,0,-32767 11A.3 Circular Polarizer #266,0,-32767 11A.4 Elliptical Polarization #267,0,-32767 11A.5 Brewster’s Angle and s- and p-Polarizations #268,0,-32767 11.3 Gaussian Beams #268,0,-32767 Lab 11B Laser Beams #271,0,-32767 11B.1 Focusing a Beam and f-Number #271,0,-32767 11B.2 The Airy Pattern and How to Clean Up a Beam #272,0,-32767 11B.3 The Mathematical Structure of Gaussian Beams #272,0,-32767 12 Vacuum #276,0,-32767 12.1 Introduction #276,0,-32767 13 Particle Detection #280,0,-32767 13.1 Introduction to Radioactivity #280,0,-32767 13.1.1 Introduction #280,0,-32767 13.1.2 Activity #281,0,-32767 Concept Tests #283,0,-32767 13.1.3 Safety #283,0,-32767 13.2 Detecting Radiation #284,0,-32767 13.2.1 GM Tubes1, #284,0,-32767 Concept Test #286,0,-32767 13.2.2 Scintillator-Based Detectors1,9 #286,0,-32767 Concept Test #287,0,-32767 13.3 Interactions with Matter #288,0,-32767 Concept Test #289,0,-32767 13.4 Counting Statistics #289,0,-32767 Concept Test #292,0,-32767 13.5 Homework Problems #292,0,-32767 Lab 13A Experiment on Counting Statistics #294,0,-32767 13A.1 Objectives #294,0,-32767 13A.2 Safety #295,0,-32767 13A.3 Experiments #295,0,-32767 13A.3.1 Background Measurement #295,0,-32767 13A.3.2 Poisson and Gaussian Distributions #296,0,-32767 13A.3.3 Measurement of GM Tube Dead Time #296,0,-32767 13A.3.4 Measuring Count Rate vs. Distance #297,0,-32767 13A.3.5 Measuring Count Rate vs. Absorber Thickness #297,0,-32767Part III Fields of Physics #300,0,-32767 14 Development and Supervision of Independent Projects #302,0,-32767 14.1 Introduction #302,0,-32767 14.2 Project Proposal #303,0,-32767 14.2.1 Research Goals #303,0,-32767 14.2.2 Literature Review #305,0,-32767 14.2.3 Work Plan #305,0,-32767 14.2.4 Equipment and Infrastructure #307,0,-32767 14.2.5 Summary #309,0,-32767 14.3 Additional Elements to Consider for an Independent Project #309,0,-32767 14.3.1 Navigating Group Dynamics #309,0,-32767 14.3.2 Weekly Planning #310,0,-32767 14.3.3 Troubleshooting #311,0,-32767 14.3.4 Summary #311,0,-32767 15 Condensed Matter Physics #312,0,-32767 15.1 Introduction #312,0,-32767 15.2 Equivalent Noise Bandwidth for a Measurement Chain #313,0,-32767 Measuring B #313,0,-32767 Method 1: Entire Chain #313,0,-32767 Method 2: Values of f3dB for Each Filter or Effective Filter #314,0,-32767 Lab 15A Quantitative Measurement of Johnson Noise #314,0,-32767 Pre-Lab Question 15A.1 #315,0,-32767 Experimental Considerations #317,0,-32767 Pre-Lab Question 15A.2: Why Should the Box Be Grounded? #318,0,-32767 Pre-Lab Question 15A.3 #319,0,-32767 Uncertainty Analysis #319,0,-32767 16 Biophysics #320,0,-32767 16.1 Introduction #320,0,-32767 Lab 16A Navigation in the Drosophila larva #321,0,-32767 Chemical Sensing and Response #321,0,-32767 Hardware Assembly #322,0,-32767 Computer Software #323,0,-32767 Odor Stimulus Delivery #323,0,-32767 An Alternative Stimulus #323,0,-32767 Fly Maintenance and Larva Selection #324,0,-32767 Control Experiments #324,0,-32767 Chemotaxis Experiments #327,0,-32767 Lab 16B Biophysics: Modeling and Stimulating Behavior #328,0,-32767 Random Walks #329,0,-32767 Diffusion #330,0,-32767 Two-Dimensional Random Walks #331,0,-32767 Simulated Control Experiments #332,0,-32767 Simulated Chemotaxis: Elements of Navigation Strategy #335,0,-32767 Lab 16C Biomechanics: Modeling Physical Actions #336,0,-32767 17 Non-Linear, Granular, and Fluid Physics #340,0,-32767 17.1 Introduction #341,0,-32767 Further Reading #342,0,-32767 Lab 17A: Drop Pinch-Off #342,0,-32767 Introduction #342,0,-32767 Objectives Shared with Other Areas of Experimental Physics #342,0,-32767 Goals of This Experiment #342,0,-32767 Time Requirements #343,0,-32767 Safety Precautions #343,0,-32767 Readings #343,0,-32767 Suggested Additional References #343,0,-32767 Introduction to Fluid Dynamics #343,0,-32767 Exercise #344,0,-32767 Surface Tension #344,0,-32767 Exercises #344,0,-32767 A Simple Model of Drop Pinch-Off #345,0,-32767 Exercises #345,0,-32767 Polymers and the Maxwell Model #346,0,-32767 Exercises #347,0,-32767 Part I: Low-Viscosity Newtonian Pinch-Off #347,0,-32767 The Trigger and Strobe #348,0,-32767 Preparing the Newtonian Fluid
