Illinois Physics 498: Introduction to Biological Physics

By Paul R Selvin

University of Illinois at Urbana-Champaign



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image 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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Researchers should cite this work as follows:

  • Paul R Selvin (2008), "Illinois Physics 498: Introduction to Biological Physics,"

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Lecture Number/Topic Online Lecture Video Lecture Notes Supplemental Material Suggested Exercises
Lecture 1: Introduction to Biophysics Notes (pdf)
Understanding biology using simple ideas from physics

Lecture 2: Central Dogma of Biology; Partition Function Notes (pdf)
Nucleic Acids, DNA,RNA, Cell size, Nucleotides, Boltzman factor, Partition function

Lecture 3: Nucleic Acids, RNA, and Proteins View Flash Notes (pdf)
Nucleic Acids, Proteins, DNA Dimensions and Stability, How to make a nucleotide

Lecture 4 : Applications of DNA Technology: FISH, PCR, Forensics View Flash Notes (pdf)
FISH (Florescence In Situ Hybridization), Gene Arrays("Chips") can be made

Lecture 5: Magnetic Traps & DNA View Flash Notes (pdf)
Introduction I

Lecture 6: Magnetic Tweezers View Flash Notes (pdf)
Introduction II and Applications

Lecture 7: Single-Molecule of ATPase Notes (pdf)
ATPase - How it produces ATP?

Lecture 8: Resolutions View Flash
X-ray diffraction (atomic resolution) Electron (Imaging) Microscopy (nm-scale) Visible (Imaging) Microscopy (nm - µm)

Lecture 9: X-ray Structure and FIONA View Flash
Accuracy vs. Resolution Measuring atomic distances Biomolecular Motors: Intra- AND Extra-Cellular Motion

Lecture 10: Mutagenesis Notes (pdf)
Site-Directed Mutagenesis to Isolate and Mutate DNA (for FIONA)

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

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...

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...

Lecture 14: FRET and Helicase Activity View Flash View Notes (pdf)
FRET: measuring conformational changes of (single) biomolecules, Unzipping mystery of helicases

Lecture 15: Confocal and STED Microscopy View Flash Notes (pdf)
Confocal Detection, Energy Transfer, Confocal Microscopy, STED (Stimulated Emission Depletion),Improved resolution

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

Lecture 17: Diffusion - Part 1 View Flash View Notes (pdf)
Diffusion, Directed motors, Thermal motion, nerve synapse, Efficiency of Diffusion

Lecture 18: Magnetotaxis Notes (pdf)
Biochemical Mechanisms for Magnetic Orientation in Animals, guest lecture Klaus Schulten.

Lecture 19: Optical Traps - Part2 View Notes (pdf)
Biological application of optical traps, High resolution optical trapping, Brownian noise

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,

Lecture 21: Nerves View Flash View Notes (pdf)
Ion Channels,Ionic current, Gating current, Digital Ion Channels, Structural studies, X-ray Crystallography

Lecture 22: Conformational Changes in Ion Channels View Flash Notes (pdf)
Voltage dependence, Spontaneous shut-off, Nerve Impulse propagation, Structure Pore Domain, Voltage Sensor

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

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