Instrumentation and Measurement for Biological Systems

Readings

• 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)
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• 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.
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• 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.
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• SantaLucia, J. “A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics.” PNAS 95, no. 4 (February 17, 1998): 1460-1465.
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• Strang, G. “Analytical Methods.” Chapter 4 in Introduction to Applied Mathematics . Wellesley, MA: Wellesley-Cambridge Press, 1986. ISBN: 9780961408800.
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• FFT Reference Material
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• 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.
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• 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.
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• Binnig, G., and C. F. Quate. “Atomic Force Microscope.” Physical Review Letters 56, no. 9 (March 3, 1986): 930-933.
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• 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.
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• Lecture slides
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• Online microscopy references
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• Papers referenced in the lab manual
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• Vukusic, P., and J. R. Sambles. “Photonic Structures in Biology.” Nature 424 (August 14, 2003): 852-856.
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• Mason, T. G. “Estimating the Viscoelastic Moduli of Complex Fluids using the Generalized Stokes-Einstein Equation.” Rheol Acta 39 (2000): 371-378.
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• 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.
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• Three papers about peacock feathers
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• Zi, Jian, et al. “Coloration Strategies in Peacock Feathers.” PNAS 100 (2003): 12576-12578.
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• Yoshioka, S., and S. Kinoshita. “Effect of Macroscopic Structure in Iridescent Color of the Peacock Feathers.” Forma 17 (2002): 169-181.
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• Kinoshita, S., and Yoshioka. “Structural Colors in Nature: The Role of Regularity and Irregularity in the Structure.” ChemPhysChem 6 (2005): 1442-1459.
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• Hong, J. W., et al. “A Nanoliter-scale Nucleic Acid Processor with Parallel Architecture.” Nature Biotech 22, no. 4 (2004): 435-439.
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• 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.
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• Winfree, E., et al. “Design and Self-assembly of Two-dimensional DNA Crystals.” Nature 394, no. 6693 (1998): 539-544.
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• Rothemund, P. W. K. “Folding DNA to Create Nanoscale Shapes and Patterns.” Nature 440, no. 7082 (2006): 297-302.
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• Hou, C. S. J., et al. “Label-free Microelectronic PCR Quantification.” Analytical Chemistry 78, no. 8 (2006): 2526-2531.
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• 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.
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• 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.
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• Schwesinger, F., et al. “Unbinding Forces of Single Antibody-Antigen Complexes Correlate with their Thermal Dissociation Rates.” PNAS 97, no. 18 (2000): 9972-9977.
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• Rugar, D., et al. “Single Spin Detection by Magnetic Resonance Force Microscopy.” Nature 430, no. 6997 (2004): 329-332.
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• Verveer, P. J., et al. “Quantitative Imaging of Lateral ErbB1 Receptor Signal Propagation in the Plasma Membrane.” Science 290 (2000): 1567-70.
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• Chen, C. S., et al. “Geometric Control of Cell Life and Death.” Science 276 (1997): 1425-28.
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• Perlman, Z. E., et al. “Multidimensional Drug Profiling by Automated Microscopy.” Science 306 (2004): 1194-98.
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• Wang, Y., et al. “Visualizing the Mechanical Activation of Src.” Nature 434 (2005): 1040-45.
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• Fritz, J., et al. “Translating Biomolecular Recognition into Nanomechanics.” Science 288, no. 5464 (2000): 316-318.
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• Axelrod, D. “Total Internal Reflection Fluorescence Microscopy in Cell Biology.” Traffic 2 (2001): 764-774.
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• 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.
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• Van Marion, A. M. W., et al. “Morphology of the Bone Marrow after Stem Cell Transplantation.” Histopahology 48 (2006): 329-42.
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• Fantner, G. E., et al. “Sacrificial Bonds and Hidden Length: Unraveling Molecular Mesostructures in Tough Materials.” Biophys J 90, no. 4 (2006): 1411-1418.
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• Block, S. M., et al. “Probing the Kinesin Reaction Cycle with a 2D Optical Force Clamp.” PNAS 100, no. 5 (2003): 2351-56.
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• 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.
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• 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.
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• Crocker, J. C., et al. “Two-point Microrheology of Inhomogeneous Soft Materials” Phys Rev Lett 85, no. 4 (2000): 888-91.
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• 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.
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• Miller, M. J., et al. “Two-photon Imaging of Lymphocyte Motility and Antigen Response in Intact Lymph Node.” Science 296 (2002): 1869-73.
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• Ichimura, T., et al. “Application of Tip-enhanced Microscopy for Nonlinear Raman Spectroscopy.” Appl Phys Lett 84, no. 10 (2004): 1768-70.
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• 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.
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• 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.
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• 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.
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• 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.
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