Illinois Physics 498: Introduction to Biological Physics
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Abstract
We will apply simple yet powerful ideas of physics to gain some understanding of biology. (What is the inertia of a bacteria and how does this affect its behavior?) We will begin with atoms, move to molecules, then macromolecules, then cells, and finally whole systems. For example, how do we see? The answer: photons cause the release of chemicals that create electricity. How do we move? The answer: tiny biomolecular motors break chemical bonds, using the energy to create force and motion with efficiencies that put man-made machines to shame. These motors, and indeed, much of biology at the molecular level, operate at the nanometer (one-billionth of a meter) and picoNewton (1 trillionth of a pound) scales. How can we measure such tiny things? Come find out! No prior biology knowledge or prerequisites, since the course includes a molecular biology primer.
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Physics 498: Introduction to Biological Physics, Spring 08
University of Illinois, Urbana-Champaign, IL
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Lecture Number/Topic | Online Lecture | Video | Lecture Notes | Supplemental Material | Suggested Exercises |
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Lecture 1: Introduction to Biophysics | Notes (pdf) | ||||
Understanding biology using simple ideas from physics |
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Lecture 2: Central Dogma of Biology; Partition Function | Notes (pdf) | ||||
Nucleic Acids, DNA,RNA, Cell size, Nucleotides, Boltzman factor, Partition function |
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Lecture 3: Nucleic Acids, RNA, and Proteins | View Flash | Notes (pdf) | |||
Nucleic Acids, Proteins, DNA Dimensions and Stability, How to make a nucleotide |
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Lecture 4 : Applications of DNA Technology: FISH, PCR, Forensics | View Flash | Notes (pdf) | |||
FISH (Florescence In Situ Hybridization), Gene Arrays("Chips") can be made |
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Lecture 5: Magnetic Traps & DNA | View Flash | Notes (pdf) | |||
Introduction I |
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Lecture 6: Magnetic Tweezers | View Flash | Notes (pdf) | |||
Introduction II and Applications |
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Lecture 7: Single-Molecule of ATPase | Notes (pdf) | ||||
ATPase - How it produces ATP? |
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Lecture 8: Resolutions | View Flash | ||||
X-ray diffraction (atomic resolution)
Electron (Imaging) Microscopy (nm-scale)
Visible (Imaging) Microscopy (nm - µm) |
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Lecture 9: X-ray Structure and FIONA | View Flash | ||||
Accuracy vs. Resolution Measuring atomic distances Biomolecular Motors: Intra- AND Extra-Cellular Motion |
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Lecture 10: Mutagenesis | Notes (pdf) | ||||
Site-Directed Mutagenesis to Isolate and Mutate DNA (for FIONA) |
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Lecture 11: FIONA (Fluorescence Imaging with One Nanometer Accuracy) | View | Notes (pdf) Notes (ppt) | |||
Fluorescence Imaging with One Nanometer Accuracy, Specificity to look at heads Nanometer spatial localization, Second temporal resolution, Single Molecule sensitivity Single Molecule Photostability |
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Lecture 12: Ultra-Resolution | View | Notes (pdf) Notes (ppt) | |||
SHREC (Single molecule High Resolution Co localization), SHRIMP (Super-High Resolution Imaging with Photobleaching), DOPI (Defocused Orientation Position Imaging), PALM (PhotoActivated Localization... |
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Lecture 13: Enhancing Resolution - FIONA - SHREC - DOPI - PALM - STORM | Notes (pdf) Notes (ppt) | ||||
Current Methods of obtaining higher resolution using: FIONA : Flouresence Imaging with One Nanometer Accuracy SHREC : Single molecule High Resolution Co-localization DOPI : Defocused Orientation... |
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Lecture 14: FRET and Helicase Activity | View Flash | View | Notes (pdf) | ||
FRET: measuring conformational changes of (single) biomolecules, Unzipping mystery of helicases |
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Lecture 15: Confocal and STED Microscopy | View Flash | Notes (pdf) | |||
Confocal Detection, Energy Transfer, Confocal Microscopy, STED (Stimulated Emission Depletion),Improved resolution |
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Lecture 16: Optical Traps - Part 1 | View Flash | View | Notes (pdf) | ||
First Optical Trap built, Reflection, Refraction, Brownian motionYann Chemla - Assistant Professor of Physics - University of Illinois at Champaign-Urbana |
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Lecture 17: Diffusion - Part 1 | View Flash | View | Notes (pdf) | ||
Diffusion, Directed motors, Thermal motion, nerve synapse, Efficiency of Diffusion |
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Lecture 18: Magnetotaxis | Notes (pdf) | ||||
Biochemical Mechanisms for Magnetic Orientation in Animals, guest lecture Klaus Schulten. |
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Lecture 19: Optical Traps - Part2 | View | Notes (pdf) | |||
Biological application of optical traps, High resolution optical trapping, Brownian noise |
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Lecture 20: Diffusion - Part2 | View Flash | View | Notes (pdf) | ||
Diffusion and bacteria moving, power consumed by bacteria, Introduction to Reynolds number, Where Bacteria Live, How E. Coli move and swim, |
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Lecture 21: Nerves | View Flash | View | Notes (pdf) | ||
Ion Channels,Ionic current, Gating current, Digital Ion Channels, Structural studies, X-ray Crystallography |
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Lecture 22: Conformational Changes in Ion Channels | View Flash | Notes (pdf) | |||
Voltage dependence, Spontaneous shut-off, Nerve Impulse propagation, Structure Pore Domain, Voltage Sensor |
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Lecture 23: Vision | View Flash | View | Notes (pdf) | ||
Summary of Ion Channels, Vision , Visual System, The Eye, Structure of the Eye, Signal Processing, Diffraction and Pupil |
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Lecture 24: The 4 Molecules of life | View Flash | View | Notes (pdf) | ||
Atoms, Molecules, Macromolecules, you!
Amino Acids, Sugars used as signals, Fatty Acids/Lipids |