Readings

This page presents a table of suggested readings for each lecture/lab session, plus slides used in a few lectures in Part III: Optics. Following the table is a list of papers suggested for student oral presentations.

WEEK # LECTURES LABS READINGS
Part I: Electronics (Instructor - Scott Manalis)
0 Course overview, procedures, syllabus, scheduling Lab orientation and tour, safety, introduction to electronics
1

Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits

RC circuits: transfer functions, Laplace transforms, impedance, RC filters

Lab orientation and tour, safety, introduction to electronics (cont.)

Module 0: introduction to electronics

Buy at Amazon Agarwal, A., and J. H. Lang. Foundations of Analog and Digital Electronic Circuits. San Diego, CA: Morgan Kaufmann, 2005, chapters 2, 3, 9, and 10. ISBN: 9781558607354.
(Resistors, capacitors, voltage and current dividers, RC transients)

This brief Diode Primer will be helpful for working on this week's lab.

Buy at Amazon Agarwal, A., and J. H. Lang. "Sinusoidal Steady State." Chapter 13 in Foundations of Analog and Digital Electronic Circuits. San Diego, CA: Morgan Kaufmann, 2005. ISBN: 9781558607354.
2

Feedback: Black's formula, the loop; Op-amps: "Golden Rules" and circuit examples

DNA analysis: SNP detection, chemical equilibrium - K and DeltaG; description of DNA melting lab apparatus

Module 1: measuring DNA melting curves

Part I: build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal

Buy at Amazon Agarwal, A., and J. H. Lang. "The Operational Amplifier Abstraction." Chapter 15 in Foundations of Analog and Digital Electronic Circuits. San Diego, CA: Morgan Kaufmann, 2005. ISBN: 9781558607354.

SantaLucia, J. "A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics." PNAS 95, no. 4 (February 17, 1998): 1460-1465.
3

Fourier series, integrals, Fourier transform (continuous/discrete)

Fourier analysis (cont.)

Evening session: student presentations 1

Module 1: measuring DNA melting curves (cont.)

Part II: complete DNA melting curves apparatus; test perfect-match, all-mismatch, and single-base mismatch DNA strands

Buy at Amazon Strang, G. "Analytical Methods." Chapter 4 in Introduction to Applied Mathematics. Wellesley, MA: Wellesley-Cambridge Press, 1986. ISBN: 9780961408800.

FFT Reference Material

Buy at Amazon W. H., et al. "Introduction," and "Fourier Transform of Discretely Sampled Data;" Chapter 12.0-12.1 and "Power Spectrum Estimation Using the FFT." Chapter 13.4 in Press, Numerical Recipes in C: The Art of Scientific Computing. 2nd ed. Cambridge, UK: Cambridge University Press, 1992. ISBN: 9780521431088.

Taton, T. A., C. A. Mirkin, and R. L. Letsinger. "Scanometric DNA Array Detection with Nanoparticle Probes." Science 289, no. 5485 (September 8, 2000): 1757-1760.
Part II: Mechanics (Instructor - Scott Manalis)
4

Scanning probe microscopy

Signals, noise, power spectral density

Module 2: atomic force microscope

Part I: AFM alignment and calibration, AFM imaging I

Binnig, G., and C. F. Quate. "Atomic Force Microscope." Physical Review Letters 56, no. 9 (March 3, 1986): 930-933.

This helpful link discusses Spectral Leakage when doing spectral analysis.

See also the above FFT reference material.
5 Correlation/convolution, lock-In amplification, linear systems

Module 2: atomic force microscope (cont.)

Part II: AFM imaging II; force spectroscopy

Tutorial 1: discrete and continuous signals, digital sampling, summary of Fourier transforms (PDF)

Tutorial 2: sampling example in Fourier space (PDF)

Convolution clarification examples (PDF)
6

Equipartition theorem and thermal fluctuations

Student presentations 2

Module 2: atomic force microscope (cont.)

Part III: thermal fluctuations of microcantilevers: Boltzmann's constant experiment

  
Part III: Optics (Instructor - Peter So)
7

Image processing I

Image processing II

 Image processing with MATLAB® (linked to homework 3)

Mathworks' MATLAB® Matrix Indexing Tutorial

Buy at Amazon Gonzalez, R., and R. E. Woods. "Histograms, Contrast, Spatial Filtering" Chapter 4, "Morphological Operations" Chapter 8, "Segmentation" Chapter 7, and "Recognition & Interpretation" Chapter 9 in Digital Image Processing. 2nd ed. East Rutherford, NJ: Prentice-Hall, 2002. ISBN: 9780201180756.
8

Physical optics and optical instrumentation: detectors, noise

Optical instrumentation: sources, lasers

 Optoelectronics: PMT and photon counting (linked to homework 3.5)

Lecture slides

(PDF 1 - 1.9 MB)

(PDF 2)
9

Introduction to microscopy: geometric optics, lenses, ray tracing

Interference and diffraction, resolution in microscopy, Fourier optics

Module 3: fluorescence microscope construction

Part I: white light imaging and Fourier optics

Lecture slides

Introduction to microscopy: geometric optics, lenses, ray tracing (This resource may not render correctly in a screen reader.PDF - 1.1 MB)

Interference and diffraction, resolution in microscopy, Fourier optics (This resource may not render correctly in a screen reader.PDF - 1.0 MB)

Online microscopy references

MicroscopyU (Nikon)

Molecular Expressions Optical Microscopy Primer
10

Fluorescence microscopy

Active microrheology

Evening session: student presentations: session 3

Module 3: fluorescence microscope construction (cont.)

Part II: live-cell imaging - microrheology

Lecture slides

(This resource may not render correctly in a screen reader.PDF - 3.3 MB)
11 Passive microrheology and particle tracking

Module 3: fluorescence microscope construction (cont.)

Part III: actin cytoskeleton imaging

MATLAB® scripts for calculating MSD and G* (ZIP) (Courtesy of Maxine Jonas. Used with permission.) (The ZIP file contains: GetGstar.m and GetMSD.m.)

Papers referenced in the lab manual

Vukusic, P., and J. R. Sambles. "Photonic Structures in Biology." Nature 424 (August 14, 2003): 852-856.

Mason, T. G. "Estimating the Viscoelastic Moduli of Complex Fluids using the Generalized Stokes-Einstein Equation." Rheol Acta 39 (2000): 371-378.

Lau, A. W. C., et al. "Microrheology, Stress Fluctuations, and Active Behavior of Living Cells." Physical Review Letters 91 no. 19 (7 November 2003): 198101.

Three papers about peacock feathers

Zi, Jian, et al. "Coloration Strategies in Peacock Feathers." PNAS 100 (2003): 12576-12578.

Yoshioka, S., and S. Kinoshita. "Effect of Macroscopic Structure in Iridescent Color of the Peacock Feathers." Forma 17 (2002): 169-181.

Kinoshita, S., and Yoshioka. "Structural Colors in Nature: The Role of Regularity and Irregularity in the Structure." ChemPhysChem 6 (2005): 1442-1459.
12

Optical trapping [Instructor: Prof. Matt Lang]

Advanced fluorescence microscopy

Evening session: student presentations 4

Module 3: fluorescence microscope construction (cont.) and experiments

Module 4: optical trapping

  
13

3D microscopy: confocal imaging

3D Microscopy: two-photon microscopy, 3D image processing

Module 4: optical trapping (cont.)

3D imaging and visualization: two-photon microscopy

 
14 Student presentations 5 3D image-stack visualization, imageJ  

 

Papers Suggested for Student Oral Presentations

Session 1

Hong, J. W., et al. "A Nanoliter-scale Nucleic Acid Processor with Parallel Architecture." Nature Biotech 22, no. 4 (2004): 435-439.

Nam, J. M., C. S. Thaxton, and C. A. Mirkin. "Nanoparticle-based Bio-bar Codes for the Ultrasensitive Detection of Proteins." Science 301, no. 5641 (2003): 1884-1886.

Winfree, E., et al. "Design and Self-assembly of Two-dimensional DNA Crystals." Nature 394, no. 6693 (1998): 539-544.

Rothemund, P. W. K. "Folding DNA to Create Nanoscale Shapes and Patterns." Nature 440, no. 7082 (2006): 297-302.

Hou, C. S. J., et al. "Label-free Microelectronic PCR Quantification." Analytical Chemistry 78, no. 8 (2006): 2526-2531.

Lai, R. Y., et al. "Rapid, Sequence-specific Detection of Unpurified PCR Amplicons via a Reusable, Electrochemical Sensor." PNAS 103, no. 11 (2006): 4017-4021.

Session 2

Engell, A., and D. J. Muller. "Observing Single Biomolecules at Work with the Atomic Force Microscope." Nature Stuct Biol 7, no. 9 (2000): 715-718.

Schwesinger, F., et al. "Unbinding Forces of Single Antibody-Antigen Complexes Correlate with their Thermal Dissociation Rates." PNAS 97, no. 18 (2000): 9972-9977.

Rugar, D., et al. "Single Spin Detection by Magnetic Resonance Force Microscopy." Nature 430, no. 6997 (2004): 329-332.

Session 3

Verveer, P. J., et al. "Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane." Science 290 (2000): 1567-70.

Chen, C. S., et al. "Geometric Control of Cell Life and Death." Science 276 (1997): 1425-28.

Perlman, Z. E., et al. "Multidimensional Drug Profiling by Automated Microscopy." Science 306 (2004): 1194-98.

Wang, Y., et al. "Visualizing the Mechanical Activation of Src." Nature 434 (2005): 1040-45.

Fritz, J., et al. "Translating Biomolecular Recognition into Nanomechanics." Science 288, no. 5464 (2000): 316-318.

Axelrod, D. "Total Internal Reflection Fluorescence Microscopy in Cell Biology." Traffic 2 (2001): 764-774.

Chung, E., D. Kim, D., and P. T. C. So. "Extended Resolution Wide-field Optical Imaging: Objective-launched Standing-wave Total Internal Reflection Fluorescence Microscopy." Opt Lett 31, no. 7 (2006): 945-7.

Van Marion, A. M. W., et al. "Morphology of the Bone Marrow after Stem Cell Transplantation." Histopahology 48 (2006): 329-42.

Session 4

Fantner, G. E., et al. "Sacrificial Bonds and Hidden Length: Unraveling Molecular Mesostructures in Tough Materials." Biophys J 90, no. 4 (2006): 1411-1418.

Block, S. M., et al. "Probing the Kinesin Reaction Cycle with a 2D Optical Force Clamp." PNAS 100, no. 5 (2003): 2351-56.

Yamada, S., D. Wirtz, and S. C. Kuo. "Mechanics of Living Cells Measured by Laser Tracking Microrheology." Biophys J 78, no. 4 (2000): 1736-47.

Yap, B., and R. D. Kamm. "Cytoskeletal Remodeling and Cellular Activation during Deformation of Neutrophils into Narrow Channels." J Appl Physiol 99 (2005): 2323-30.

Crocker, J. C., et al. "Two-point Microrheology of Inhomogeneous Soft Materials" Phys Rev Lett 85, no. 4 (2000): 888-91.

Rousso, I., et al. "Microsecond Atomic Force Sensing of Protein Conformational Dynamics: Implications for the Primary Light-induced Events in Bacteriorhodopsin." PNAS 94 (1997): 7937-41.

Session 5

Miller, M. J., et al. "Two-photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node." Science 296 (2002): 1869-73.

Ichimura, T., et al. "Application of Tip-enhanced Microscopy for Nonlinear Raman Spectroscopy." Appl Phys Lett 84, no. 10 (2004): 1768-70.

Koo, T-W., S. Chan, and A. A. Berlin. "Single-molecule Detection of Biomolecules by Surface-enhanced Coherent Anti-Stokes Raman Scattering." Opt Lett 30, no. 9 (2005): 1024-6.

Wang, H., et al. "Coherent Anti-Stokes Raman Scattering Imaging of Axonal Myelin in Live Spinal Tissues" Biophys J 89, no. 1 (2005): 581-91.

Hanson, K. M., et al. "Two-photon Fluorescence Lifetime Imaging of the Skin Stratum Corneum pH Gradient." Biophys J 83, no. 3 (2002): 1682-90.

Campagnola, P. J., et al. "Three-dimensional High-resolution Second-harmonic Generation Imaging of Endogenous Structural Proteins in Biological Tissues." Biophys J 81, no. 1 (2002): 493-508.